Transition State Research Articles

Study on dynamic behavior of atomic diffusion at interface between TiAlN coating and WC matrix

Abstract The molecular dynamics method was used to simulate the dynamic behavior change of atomic diffusion at interface between TiAlN coating and WC matrix in the carbide tool with TiAlN coating. It was determined that the one-way diffusion of C atom to TiAlN coating resulted in serious lattice distortion on the surface. Meanwhile, the whole diffusion process was accompanied by the continuous increase of stress, resulting in gradual deformation of the material. The interface bonding performance also decreases. Then, the surface energy and atomic layer convergence are calculated by the first-principles method. The TiAlN crystal surface is stable at 8 atomic layers, and the WC crystal surface is stable at 6 atomic layers, and then a stable microinterface model can be built. The relaxation processing for the established model was performed to determine the diffusion path of C atom. Then, the energy barrier, adhesion work, interface energy and fracture toughness of different transition state structures in the diffusion path of C atom are calculated, and it is determined that with the deepening of the diffusion of C atom in the coating, the binding ability of the interface of the coating base and the performance of the coating tool are more and more serious damage. Finally, the cutting experiment of TiAlN coated tool is designed. According to the surface topography of TiALN coated tool in different periods, the simulation and theoretical analysis mentioned above are verified, which provides a theoretical basis for the subsequent research on improving the performance of coated tool.

Experimentally Delineating the Catalytic Effect of a Single Water Molecule in the Photochemical Rearrangement of the Phenylperoxy Radical to the Oxepin-2(5H)-one-5-yl Radical.

Catalysis plays a pivotal role in both chemistry and biology, primarily attributed to its ability to stabilize transition states and lower activation free energies, thereby accelerating reaction rates. While computational studies have contributed valuable mechanistic insights, there remains a scarcity of experimental investigations into transition states. In this work, we embark on an experimental exploration of the catalytic energy lowering associated with transition states in the photorearrangement of the phenylperoxy radical-water complex to the oxepin-2(5H)-one-5-yl radical. Employing matrix isolation spectroscopy, density functional theory, and post-HF computations, we scrutinize the (photo)catalytic impact of a single water molecule on the rearrangement. Our computations indicate that the barrier heights for the water-assisted unimolecular isomerization steps are approximately 2-3 kcal mol-1 lower compared to the uncatalyzed steps. This decrease directly coincides with the energy difference in the required wavelength during the transformation (Δλ = λ546nm - λ579nm ≡ 52.4-49.4 = 3.0 kcal mol-1), allowing us to elucidate the differential transition state energy in the photochemical rearrangement of the phenylperoxy radical catalyzed by a single water molecule. Our work highlights the important role of water catalysis and has, among others, implications for understanding the mechanism of organic reactions under atmospheric conditions.

How Droplets Can Accelerate Reactions─Coacervate Protocells as Catalytic Microcompartments.

ConspectusCoacervates are droplets formed by liquid-liquid phase separation (LLPS) and are often used as model protocells-primitive cell-like compartments that could have aided the emergence of life. Their continued presence as membraneless organelles in modern cells gives further credit to their relevance. The local physicochemical environment inside coacervates is distinctly different from the surrounding dilute solution and offers an interesting microenvironment for prebiotic reactions. Coacervates can selectively take up reactants and enhance their effective concentration, stabilize products, destabilize reactants and lower transition states, and can therefore play a similar role as micellar catalysts in providing rate enhancement and selectivity in reaction outcome. Rate enhancement and selectivity must have been essential for the origins of life by enabling chemical reactions to occur at appreciable rates and overcoming competition from hydrolysis.In this Accounts, we dissect the mechanisms by which coacervate protocells can accelerate reactions and provide selectivity. These mechanisms can similarly be exploited by membraneless organelles to control cellular processes. First, coacervates can affect the local concentration of reactants and accelerate reactions by copartitioning of reactants or exclusion of a product or inhibitor. Second, the local environment inside the coacervate can change the energy landscape for reactions taking place inside the droplets. The coacervate is more apolar than the surrounding solution and often rich in charged moieties, which can affect the stability of reactants, transition states and products. The crowded nature of the droplets can favor complexation of large molecules such as ribozymes. Their locally different proton and water activity can facilitate reactions involving a (de)protonation step, condensation reactions and reactions that are sensitive to hydrolysis. Not only the coacervate core, but also the surface can accelerate reactions and provides an interesting site for chemical reactions with gradients in pH, water activity and charge. The coacervate is often rich in catalytic amino acids and can localize catalysts like divalent metal ions, leading to further rate enhancement inside the droplets. Lastly, these coacervate properties can favor certain reaction pathways, and thereby give selectivity over the reaction outcome.These mechanisms are further illustrated with a case study on ribozyme reactions inside coacervates, for which there is a fine balance between concentration and reactivity that can be tuned by the coacervate composition. Furthermore, coacervates can both catalyze ribozyme reactions and provide product selectivity, demonstrating that coacervates could have functioned as enzyme-like catalytic microcompartments at the origins of life.

Accurate NMR Shieldings with σ-Functionals.

In recent years, density-functional methods relying on a new type of fifth-rung correlation functionals called σ-functionals have been introduced. σ-Functionals are technically closely related to the random phase approximation and require the same computational effort but yield distinctively higher accuracies for reaction and transition state energies of main group chemistry and even outperform double-hybrid functionals for these energies. In this work, we systematically investigate how accurate σ-functionals can describe nuclear magnetic resonance (NMR) shieldings. It turns out that σ-functionals yield very accurate NMR shieldings, even though in their optimization, exclusively, energies are employed as reference data and response properties such as NMR shieldings are not involved at all. This shows that σ-functionals combine universal applicability with accuracy. Indeed, the NMR shieldings from a σ-functional using input orbitals and eigenvalues from Kohn-Sham calculations with the exchange-correlation functional of Perdew, Burke and Ernzerhof (PBE) turned out to be the most accurate ones among the NMR shieldings calculated with various density-functional methods including methods using double-hybrid functionals. That σ-functionals can be used for calculating both reliable energies and response properties like NMR shieldings characterizes them as all-purpose functionals, which is appealing from an application point of view.

Predicting decomposition temperatures and carbonization feasibility of heterocycles with their decomposition mechanism

Pyrolysis of heterocyclic compounds such as Meldrum’s acid derivatives was studied with two key mechanisms analysing their energy barrier diagrams by the hybrid density functional theory method M06-2X. The feasibility of these decomposition reactions was calculated specifically for Meldrum’s acid, monomethyl Meldrum’s acid, dimethyl Meldrum’s acid (DMMA), methylene Meldrum’s acid (MeMA) and (dimethylamino)methylene Meldrum’s acid (DMAMeMA), based on previous experimental analysis. Their initial decomposition products (ketene or substituted ketenes with CO2 and acetone) were found endothermic requiring activation energies (∼180–––230 kJ/mol) at the decomposition temperatures of 280, 299, 301, 503 and 414 K respectively. The transition state theory calculations show MeMA and DMAMeMA are thermally more stable than other derivatives with low values for the rate constants and high energy barriers to produce initial decomposition products, suggesting they can produce fine carbon materials during carbonization. DMMA is found the best option for obtaining heteroatoms-doped carbon material formation.

Rationally Designed L12-Pt2RhFe Intermetallic Catalyst with High CO-Tolerance for Alkaline Methanol Electrooxidation.

It is a grand challenge to deep understanding of and precise control over functional sites for the rational design of highly efficient catalysts for methanol electrooxidation. Here, an L12-Pt2RhFe intermetallic catalyst with integrated functional components is demonstrated, which exhibits exceptional CO tolerance. The Pt2RhFe/C achieves a superior mass activity of 6.43 A mgPt -1, which is 2.23-fold and 3.53-fold higher than those of PtRu/C and Pt/C. Impressively, the Pt2RhFe/C exhibits a significant enhancement in durability owing to its high CO-tolerance and stability. Density functional theory calculations reveal that high performance of Pt2RhFe intermetallic catalyst arises from the synergistic effect: the strong OH binding energy (OHBE) at Fe sites induce stably adsorbed OH species and thus facilitate the dehydrogenation step of methanol via rapid hydrogen transfer, while moderate OHBE at Rh sites promote the formation of the transition state (Pt-CO···OH-Rh) with a low activation barrier for CO removal. This work provides new insights into the role of OH binding strength in the removal of CO species, which is beneficial for the rational design of highly efficient catalysts.

Synthesis and Ring‐Closing Reactions of Aminocyclohexane Derivatives Bearing Unsaturated Side Chains at C2: Stereocontrolled Approaches to cis‐ and trans‐Fused Perhydro‐indoles and ‐Quinolines

AbstractTwo epimeric pairs of N‐Ts‐protected cyclohexylamines that incorporate an unsaturated side‐chain at the C2 position have been prepared. Contrary to expectations, none of these underwent clean, photochemically‐induced intramolecular hydroamination reactions to give the corresponding perhydro‐indole or ‐quinolines. However, they did participate in efficient olefin cross metathesis (OCM) reactions with methyl crotonate. Three of the four acrylates so‐formed engaged in base‐promoted and completely diastereoselective, intramolecular aza‐Michael addition (cyclization) reactions to give the isomeric and C2‐substituted perhydro‐indoles or ‐quinolines with the structures of these being confirmed by single‐crystal X‐ray analyses. DFT calculations generated results consistent with the observed diastereoselectivities and the proposed transition states. Manipulation of the ester groups associated with the cyclization products allowed for their conversion, inter alia, into the corresponding n‐propyl residues and thus providing novel analogues of neurotoxic alkaloids such as pumiliotoxin C.

Novel Insights into the Catalytic Mechanism of Collagenolysis by Zn(II)-Dependent Matrix Metalloproteinase-1.

Collagen hydrolysis, catalyzed by Zn(II)-dependent matrix metalloproteinases (MMPs), is a critical physiological process. Despite previous computational investigations into the catalytic mechanisms of MMP-mediated collagenolysis, a significant knowledge gap in understanding remains regarding the influence of conformational sampling and entropic contributions at physiological temperature on enzymatic collagenolysis. In our comprehensive multilevel computational study, employing quantum mechanics/molecular mechanics (QM/MM) metadynamics (MetD) simulations, we aimed to bridge this gap and provide valuable insights into the catalytic mechanism of MMP-1. Specifically, we compared the full enzyme-substrate complex in solution, clusters in solution, and gas-phase to elucidate insights into MMP-1-catalyzed collagenolysis. Our findings reveal significant differences in the catalytic mechanism when considering thermal effects and the dynamic evolution of the system, contrasting with conventional static potential energy surface QM/MM reaction path studies. Notably, we observed a significant stabilization of the critical tetrahedral intermediate, attributed to contributions from conformational flexibility and entropy. Moreover, we found that protonation of the scissile bond nitrogen occurs via proton transfer from a Zn(II)-coordinated hydroxide rather than from a solvent water molecule. Following C-N bond cleavage, the C-terminus remains coordinated to the catalytic Zn(II), while the N-terminus forms a hydrogen bond with a solvent water molecule. Subsequently, the release of the C-terminus is facilitated by the coordination of a water molecule. Our study underscores the pivotal role of protein conformational dynamics at physiological temperature in stabilizing the transition state of the rate-limiting step and key intermediates, compared to the corresponding reaction in solution. These fundamental insights into the mechanism of collagen degradation provide valuable guidance for the development of MMP-1-specific inhibitors.

Chain-Length Dependence of Peptide-Lipid Bilayer Interaction Strength and Binding Kinetics: A Combined Theoretical and Experimental Approach.

Physical interactions between polypeptide chains and lipid membranes underlie critical cellular processes. Yet, despite fundamental importance, key mechanistic aspects of these interactions remain elusive. Bulk experiments have revealed a linear relationship between free energy and peptide chain length in a model system, but does this linearity extend to the interaction strength and to the kinetics of lipid binding? To address these questions, we utilized a combination of coarse-grained molecular dynamics (CG MD) simulations, analytical modeling, and atomic force microscopy (AFM)-based single molecule force spectroscopy. Following previous bulk experiments, we focused on interactions between short hydrophobic peptides (WLn, n = 1, ..., 5) with 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) bilayers, a simple system that probes peptide primary structure effects. Potentials of mean force extracted from CG MD recapitulated the linearity of free energy with the chain length. Simulation results were quantitatively connected to bulk biochemical experiments via a single scaling factor of order unity, corroborating the methodology. Additionally, CG MD revealed an increase in the distance to the transition state, a result that weakens the dependence of the dissociation force on the peptide chain length. AFM experiments elucidated rupture force distributions and, through modeling, intrinsic dissociation rates. Taken together, the analysis indicates a rupture force plateau in the WLn-POPC system, suggesting that the final rupture event involves the last 2 or 3 residues. In contrast, the linear dependence on chain length was preserved in the intrinsic dissociation rate. This study advances the understanding of peptide-lipid interactions and provides potentially useful insights for the design of peptides with tailored membrane-interacting properties.

Acid-base synergistic effect towards catalytic transfer hydrogenation reactions

Catalytic transfer hydrogenation (CTH) of aldehydes/ketones by using alcohols as hydrogen donors is an attractive and environmentally friendly hydrogenation technology, which has evoked widespread attention in synthesis of fine chemicals from biomass resources. In this work, a Co-Al mixed metal oxide catalyst (Co1Al2-MMO-200) was obtained through structural topological transformation process of layered double hydroxides, which was used in the CTH reaction of furfural with isopropanol. Notably, the reaction rate achieves 0.023 mol g−1 h−1, which is preponderate to acid-base catalysts earlier reported. The joint research based on CO2-TPD, NH3-TPD and poisoning experiment substantiates that the synergy effect of acid-base sites plays an essential role in this catalytic system. Isotopic labelling MS, in-situ FT-IR and DFT studies further verify that the CTH reaction of furfural occurs via the Meerwein-Ponndorf-Verley (MPV) route, in which the basic site promotes the deprotonation of isopropanol whilst the acid site facilitates the formation of a six-membered ring transition state. This work demonstrates an acid-base synergetic catalysis for the CTH reaction by revealing the structure-property correlation and exploring reaction route, which is instructive for designing high-performance heterogenous catalysts.

Steric Effect and Intrinsic Electrophilicity and Nucleophilicity from a Conceptual Density Functional Theory and Information-Theoretic Approach as Quantitative Probes of Chemical Reactions.

Appreciating reactivity in terms of physicochemical effects for chemical processesis one of the most important undertakings in chemistry. While transition state (TS) theory provides the framework enabling the reliable calculation of the barrier height for a given elementary step, analytical tools are necessary to gain insight into key factors governing the different processes during chemical reactions. In this contribution, we partition the potential energy surface of an elementary step along the intrinsic coordinate into three segments, the so-called Pre-TS, TS, and Post-TS regions, and then determine the most important factors dictating each segment. This analysis is based on the use of both reactivity descriptors from conceptual density functional theory and concepts from the information-theoretic approach in density functional theory. We found that in both Pre-TS and Post-TS regions, steric effects are the dominant factors, whereas in the TS region, it is the intrinsic electrophilic and nucleophilic propensity of the transition state structure that governs the reactivity. The wide applicability of our approach is shown by a validation for a total of 37 organic and inorganic reactions. This work thus, in our view, provides a novel perspective on how chemical reactivity can be quantified at different stages of chemical reactions.

Mechanism, thermochemistry, and kinetics of formation of PhC(O)H and HOPhC(O)H during unimolecular decomposition of P-PhC(O2•)HPhOH.

Bisphenols are one of the main components of bio-oil, produced during the pyrolysis of lignin-containing biomass. Synthetic bisphenols are used in polycarbonate plastics, epoxy resins, and thermal papers. Their mechanism of oxidation is important for the determination of the fire safety of these materials and the possibility of using them as additives in fuels for the decrease and description of ignition delays, as well as for the determination of their health risk assessment in medicine. One representative of bisphenols is p-benzylphenol (p-PhCH2PhOH), which is formed during the fast pyrolysis of lignine-containing biomass. Its thermochemistry of oxidation has been partially studied previously. It is shown that the reaction of chain oxidation of p-PhCH2PhOH is thermochemically favorable at low temperatures. However, these studies consider only two pathways of this reaction: (1) the chain oxidation of RH by RO2• and (2) the tautomerization of R'HO2• to R'O2H with following production of R'O• and OH radicals. At the same time, the reactions of intramolecular rearrangement of RO2•, produced PhC(O)H and •PhOH or HOPhC(O)H and •Ph, are not reported but can be an important part of its oxidation mechanism. The five DFT (M06-2X (i = 1), B3LYP (i = 2), wB97XD (i = 3), M08HX (i = 4), MN15 (i = 5)) approaches with 6-311 + + G(d,p) basis set are used for the determination of standard enthalpies of atomization (ΔraH°(Xi)) of considered compounds (molecules, radicals, and transition states). These values of ΔraH°(Xi) are corrected using the empirical linear calibration dependencies, reported previously. The different calibration dependencies are used for the hydrocarbons (including the aromatics and simple oxygenated derivatives) and for the peroxides. The corrected values of ΔraH°(Xi, CORR) are used according to Hess's law for the determination of ΔfH°(Xi, CORR). The most consistent values of ΔfH°(X, MEAN) are derived from the coordination of the values of ΔfH°(Xi,CORR) using the intersection of their values of standard deviations (3SDi). These values of ΔfH°(X, MEAN), as well as the B3LYP values of S°(X), which are accounting the frequencies correction and internal rotations, as well as their temperature dependencies, are used for the determination of thermochemistry of considered reactions and of the calculation, within transition state theory (TST), of the values of high pressure limits of the rate constant. The values of H°(Xi), S°(Xi), and G°(Xi) are calculated using the Gaussian 16w program. The considered mechanism is prepared using ISIS/Draw package. The temperature dependencies of thermochemical properties and the values of rate constants are determined using the ChemRate program (v.1.5). The optimized structures are visualized using the Chemcraft package.

Structural and mechanistic analysis of Ca2+-dependent regulation of transglutaminase 2 activity using a Ca2+-bound intermediate state

Mammalian transglutaminases, a family of Ca2+-dependent proteins, are implicated in a variety of diseases. For example, celiac disease (CeD) is an autoimmune disorder whose pathogenesis requires transglutaminase 2 (TG2) to deamidate select glutamine residues in diet-derived gluten peptides. Deamidation involves the formation of transient γ-glutamyl thioester intermediates. Recent studies have revealed that in addition to the deamidated gluten peptides themselves, their corresponding thioester intermediates are also pathogenically relevant. A mechanistic understanding of this relevance is hindered by the absence of any structure of Ca2+-bound TG2. We report the X-ray crystallographic structure of human TG2 bound to an inhibitory gluten peptidomimetic and two Ca2+ ions in sites previously designated as S1 and S3. Together with additional structure-guided experiments, this structure provides a mechanistic explanation for how S1 regulates formation of an inhibitory disulfide bond in TG2, while also establishing that S3 is essential for γ-glutamyl thioester formation. Furthermore, our crystallographic findings and associated analyses have revealed that i) two interacting residues, H305 and E363, play a critical role in resolving the thioester intermediate into an isopeptide bond (transamidation) but not in thioester hydrolysis (deamidation); and ii) residues N333 and K176 stabilize preferred TG2 substrates and inhibitors via hydrogen bonding to nonreactive backbone atoms. Overall, the intermediate-state conformer of TG2 reported here represents a superior model to previously characterized conformers for both transition states of the TG2-catalyzed reaction.

Rational Design of the Spatial Effect in a Fe(II)/α‐Ketoglutarate‐Dependent Dioxygenase Reverses the Regioselectivity of C(sp3)−H Bond Hydroxylation in Aliphatic Amino Acids

AbstractThe hydroxylation of remote C(sp3)−H bonds in aliphatic amino acids yields crucial precursors for the synthesis of high‐value compounds. However, accurate regulation of the regioselectivity of remote C(sp3)−H bonds hydroxylation in aliphatic amino acids continues to be a common challenge in chemosynthesis and biosynthesis. In this study, the Fe(II)/α‐ketoglutarate‐dependent dioxygenase from Bacillus subtilis (BlAH) was mined and found to catalyze hydroxylation at the γ and δ sites of aliphatic amino acids. Crystal structure analysis, molecular dynamics simulations, and quantum chemical calculations revealed that regioselectivity was regulated by the spatial effect of BlAH. Based on these results, the spatial effect of BlAH was reconstructed to stabilize the transition state at the δ site of aliphatic amino acids, thereby successfully reversing the γ site regioselectivity to the δ site. For example, the regioselectivity of L‐Homoleucine (5 a) was reversed from the γ site (1 : 12) to the δ site (>99 : 1). The present study not only expands the toolbox of biocatalysts for the regioselective functionalization of remote C(sp3)−H bonds, but also provides a theoretical guidance for the precision‐driven modification of similarly remote C(sp3)−H bonds in complex molecules.

Effect of agitation speed on methylene blue discoloration kinetics via ambient air cold plasma

AbstractThis research investigates the kinetics of methylene blue (MB) discoloration using ambient air cold plasma, with a focus on the impact of agitation speed (100 and 750 rpm). The study revealed pseudo‐first‐order kinetics for MB discoloration, pinpointing optimal conditions at 35.00°C and 100 rpm. These parameters minimized half‐life times, correlated with observed kobs values. A decreasing pH trend, more pronounced at 750 rpm, was attributed to increased acidic nitrogen species (HNO3 and HNO2) production, adversely affecting dye discoloration. Concurrently, enhanced electrolyte concentration was noted from rising conductivity due to plasma production of reactive species followed by solubilization in the aqueous phase. The calculated thermodynamic activation parameters comprised: Ea = 7.96 kJ mol−1, ΔH‡ = +5.53 kJ mol−1, ΔS‡ = −253.23 J K−1 mol−1, and ΔG‡ = +79.77 kJ mol−1 (100 rpm); and Ea = 12.94 kJ mol−1, ΔH‡ = +13.78 kJ mol−1, ΔS‡ = −239.06 J K−1 mol−1, and ΔG‡ = +80.58 kJ mol−1, (750 rpm). The lowest Ea and ΔG‡ values at 100 rpm reinforced lower agitation favoring the reaction. The study demonstrated a linear decay of the reaction rate constant with the square root of ionic strength. This result, besides the negative activation entropy and moderate activation enthalpy led to a proposition to the determinant step for the transition state formation, involving an associative step between a solvated electron and the protonated substrate. The optimal dye discoloration rate and energy yield were observed at 35.00°C and 100 rpm, with values of 97.2% and 3.371 × 10−2 g kW−1 h−1, respectively.

Oxidative Addition of (Hetero)aryl (Pseudo)halides at Palladium(0): Origin and Significance of Divergent Mechanisms.

Two limiting mechanisms are possible for oxidative addition of (hetero)aryl (pseudo)halides at Pd(0): a 3-centered concerted and a nucleophilic displacement mechanism. Until now, there has been little understanding about when each mechanism is relevant. Prior investigations to distinguish between these pathways were limited to a few specific combinations of the substrate and ligand. Here, we computationally evaluated over 180 transition structures for oxidative addition in order to determine mechanistic trends based on substrate, ligand(s), and coordination number. Natural abundance 13C kinetic isotope effects provide experimental results consistent with computational predictions. Key findings include that (1) differences in highest occupied molecular orbital (HOMO) symmetries dictate that, although 12e- PdL is strongly biased toward a 3-centered concerted mechanism, 14e- PdL2 often prefers a nucleophilic displacement mechanism; (2) ligand electronics and sterics, including ligand bite angle, influence the preferred mechanism of the reaction at PdL2; (3) phenyl triflate always reacts through a displacement mechanism regardless of the catalyst structure due to the stability of a triflate anion and the inability of oxygen to effectively donate electron density to Pd; and (4) the high reactivity of C-X bonds adjacent to nitrogen in pyridine substrates relates to stereoelectronic stabilization of a nucleophilic displacement transition state. This work has implications for controlling rate and selectivity in catalytic couplings, and we demonstrate application of the mechanistic insight toward chemodivergent cross-couplings of bromochloroheteroarenes.

Dry reforming of methane over Ni5 nanocluster supported on double perovskite surface − A DFT study

The opportunity for efficient hydrogen extraction from natural gas through perovskite-supported Ni5 nanocluster has been investigated using first-principles calculations. The reaction dynamics of dry reforming of methane (DRM) has been studied, and all the elementary steps are assessed to locate the transition states. The obtained results demonstrate a high affinity of CH4 and CO2 towards the supported nanocluster as predicted by reasonably large adsorption energies. Chromium and Molybdenum on the perovskite surface play an essential role, in conjunction with Nickel, in methane CH bond activation. Ni2Cr and Ni2Mo are identified as the sites where methane reaction begins and ends, or vice versa. The dissociation of CO2 is also facilitated by the nanocluster, with the rate-limiting step in the two pathways being CH4 dissociation. The study suggests that decorating the anode with Ni-nanoclusters can effectively promote hydrogen extraction from hydrocarbon fuels in solid-oxide fuel cells.

EVOLUTION OF ELECTRONIC PROPERTIES ALONG THE PATH FROM COVALENT TO TETREL BOND IN THE SYNTHESIS OF TETRAPHENYL SUBSTITUTED COMPOUNDS

The evolution of the electronic characteristics of chemical bonds formed and broken along the path of the bimolecular nucleophilic substitution reaction at a tetrahedral central atom, which is the Tt = C, Si, Ge atom, is analyzed. For this purpose, the reaction paths of the step-by-step replacement of the chlorine atom with the phenyl fragment have been modeled, and the energy characteristics of the equilibrium initial, transition and nal states were obtained within the framework of DFT. For different reaction centers, which are atoms of the carbon group (Tt), changes in electron density distributions, shifts in the positions of the extremes of the total static and electrostatic potential for the forming C-Tt and breaking Tt-Cl bonds along the reaction path are compared. Quantitative criteria have been re ned that determine the region of existence of a typical noncovalent tetrel bond Tt...Cl, allowing it to be distinguished from a covalent one. Establishment of the properties of the transition state stabilizing tetrel bond may be useful for monitoring the ef cient synthesis of covalent organic framework precursors.

Exploring Bacillus species xylanases for industrial applications: screening via thermostability and reaction modelling.

Xylanases derived from Bacillus species hold significant importance in various large-scale production sectors, with increasing demand driven by biofuel production. However, despite their potential, the extreme environmental conditions often encountered in production settings have led to their underutilisation. To address this issue and enhance their efficacy under adverse conditions, we conducted a theoretical investigation on a group of five Bacillus species xylanases belonging to the glycoside hydrolase GH11 family. Bacillus sp. NCL 87-6-10 (sp_NCL 87-6-10) emerged as a potent candidate among the selected biocatalysts; this Bacillus strain exhibited high thermal stability and achieved a transition state with minimal energy requirements, thereby accelerating the biocatalytic reaction process. Our approach aims to provide support for experimentalists in the industrial sector, encouraging them to employ structural-based reaction modelling scrutinisation to predict the ability of targeted xylanases. Utilising crystal structure data available in the Carbohydrate-Active enzymes database, we aimed to analyse their structural capabilities in terms of thermal-stability and activity. Our investigation into identifying the most prominent Bacillus species xylanases unfolds with the help of the semi-empirical quantum mechanics MOPAC method integrated with the DRIVER program is used in calculations of reaction pathways to understand the activation energy. Additionally, we scrutinised the selected xylanases using various analyses, including constrained network analyses, intermolecular interactions of the enzyme-substrate complex and molecular orbital assessments calculated using the AM1 method with the MO-G model (MO-G AM1) to validate their reactivity.

Theoretical insight into the sulfurated poisoning process of rhenium-doped nickel catalyst

Three rhenium-doped nickel catalyst surfaces including Re-Ni(111), Re-Ni(200) and Re-Ni(220) were built via Re atom substituting one atom of upper layer Ni surfaces. The sulfurated poisoning process involving H2S adsorption and subsequent splitting steps (H2S→HS+H, HS→S+H) on the three surfaces was investigated and further compared using density functional theory (DFT) to understand the crystal-plane effect. For H2S adsorption, the H2S molecule is preferentially adsorbed on the Re top and bridge ReNi1 sites. Re-Ni(200) surface possessed lower H2S adsorption energy compared to Re-Ni(111) and Re-Ni(220) surfaces, due to its smaller coordination number and higher d-orbital intensity at Fermi level. For splitting steps, transition state search showed that the two processes on the three surfaces are all calculated as exothermic while the energy barrier is basically in the range of 0.23 eV∼0.44 eV, which signifies that the poisoning process is favorable both kinetically and thermodynamically. The splitting steps can be described as a dynamic procedure that contains intimate HS fragment activation, S-H bond stretching accompanied by H atom departure and final dissociation into HS+H or S+H co-intermediates. The valence bond changes during dissociation deduced from projected density of states (PDOS) analysis also proved the above procedure.