Computational Study of Catalytic Urethane Formation.
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ABSTRACT:
SUBMITTER: Waleed HQ
PROVIDER: S-EPMC8747140 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The chemistry of urethanes plays a key role in important industrial processes. Although catalysts are often used, the study of the reactions without added catalysts provides the basis for a deeper understanding. For the non-catalytic urethane formation and cleavage reactions, the dominating reaction mechanism has long been debated. To our knowledge, the reaction kinetics have not been predicted quantitatively so far. Therefore, we report a new computational study of urethane formation and cleavage reactions. To analyze various potential reaction mechanisms and to predict the reaction rate constants quantum chemistry and transition state theory were employed. For validation, experimental data from literature and from own experiments were used. Quantitative agreement of experiments and predictions could be demonstrated. The calculations confirm earlier assumptions that urethane formation reactions proceed via mechanisms where alcohol molecules act as auto-catalysts. Our results show that it is essential to consider several transition states corresponding to different reaction orders to enable agreement with experimental observations. Urethane cleavage seems to be catalyzed by an isourethane, leading to an observed 2nd-order dependence of the reaction rate on the urethane concentration. The results of our study support a deeper understanding of the reactions as well as a better description of reaction kinetics and will therefore help in catalyst development and process optimization.
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Project description:The alcoholysis of phenyl isocyanate (PhNCO) using stoichiometric butan-1-ol (BuOH) in acetonitrile in the presence of different cyclic amine catalysts was examined using a combined kinetic and mechanistic approach. The molecular mechanism of urethane formation without and in the presence of cyclic amine catalysts was studied using the G3MP2BHandHLYP composite method in combination with the SMD implicit solvent model. It was found that the energetics of the model reaction significantly decreased in the presence of catalysts. The computed and measured thermodynamic properties were in good agreement with each other. The results prove that amine catalysts are important in urethane synthesis. Based on the previous and current results, the design of new catalysts will be possible in the near future.
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Project description:A kinetic and mechanistic investigation of the alcoholysis of phenyl isocyanate using 1-propanol as the alcohol was undertaken. A molecular mechanism of urethane formation in both alcohol and isocyanate excess is explored using a combination of an accurate fourth generation Gaussian thermochemistry (G4MP2) with the Solvent Model Density (SMD) implicit solvent model. These mechanisms were analyzed from an energetic point of view. According to the newly proposed two-step mechanism for isocyanate excess, allophanate is an intermediate towards urethane formation via six-centered transition state (TS) with a reaction barrier of 62.6 kJ/mol in the THF model. In the next step, synchronous 1,3-H shift between the nitrogens of allophanate and the cleavage of the C-N bond resulted in the release of the isocyanate and the formation of a urethane bond via a low-lying TS with 49.0 kJ/mol energy relative to the reactants. Arrhenius activation energies of the stoichiometric, alcohol excess and the isocyanate excess reactions were experimentally determined by means of HPLC technique. The activation energies for both the alcohol (measured in our recent work) and the isocyanate excess reactions were lower compared to that of the stoichiometric ratio, in agreement with the theoretical calculations.
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Project description:Lysine-specific demethylase 1 (LSD1), the first identified histone demethylase, is a flavin-dependent amine oxidase which specifically demethylates mono- or dimethylated H3K4 and H3K9 via a redox process. It participates in a broad spectrum of biological processes and is of high importance in cell proliferation, adipogenesis, spermatogenesis, chromosome segregation and embryonic development. To date, as a potential drug target for discovering anti-tumor drugs, the medical significance of LSD1 has been greatly appreciated. However, the catalytic mechanism for the rate-limiting reductive half-reaction in demethylation remains controversial. By employing a combined computational approach including molecular modeling, molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations, the catalytic mechanism of dimethylated H3K4 demethylation by LSD1 was characterized in details. The three-dimensional (3D) model of the complex was composed of LSD1, CoREST, and histone substrate. A 30-ns MD simulation of the model highlights the pivotal role of the conserved Tyr761 and lysine-water-flavin motif in properly orienting flavin adenine dinucleotide (FAD) with respect to substrate. The synergy of the two factors effectively stabilizes the catalytic environment and facilitated the demethylation reaction. On the basis of the reasonable consistence between simulation results and available mutagenesis data, QM/MM strategy was further employed to probe the catalytic mechanism of the reductive half-reaction in demethylation. The characteristics of the demethylation pathway determined by the potential energy surface and charge distribution analysis indicates that this reaction belongs to the direct hydride transfer mechanism. Our study provides insights into the LSD1 mechanism of reductive half-reaction in demethylation and has important implications for the discovery of regulators against LSD1 enzymes.
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Project description:By means of spin-polarized density functional theory (DFT) computations, we unravel the reaction mechanisms of catalytic CO oxidation on B-doped fullerene. It is shown that O2 species favors to be chemically adsorbed via side-on configuration at the hex-C-B site with an adsorption energy of -1.07 eV. Two traditional pathways, Eley-Rideal (ER) and Langmuir-Hinshelwood (LH) mechanisms, are considered for the CO oxidation starting from O2 adsorption. CO species is able to bind at the B-top site of the B-doped fullerene with an adsorption energy of -0.78 eV. Therefore, CO oxidation that occurs starting from CO adsorption is also taken into account. Second reaction of CO oxidation occurs by the reaction of CO + O → CO2 with a very high energy barrier of 1.56 eV. A trimolecular Eley-Rideal (TER) pathway is proposed to avoid leaving the O atom on the B-doped fullerene after the first CO oxidation. These predictions manifest that boron-doped fullerene is a potential metal-free catalyst for CO oxidation.
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Project description:A mechanistic study of the isothiourea-catalyzed enantioselective [2,3]-rearrangement of allylic ammonium ylides is described. Reaction kinetic analyses using 19F NMR and density functional theory computations have elucidated a reaction profile and allowed identification of the catalyst resting state and turnover-rate limiting step. A catalytically relevant catalyst-substrate adduct has been observed, and its constitution elucidated unambiguously by 13C and 15N isotopic labeling. Isotopic entrainment has shown the observed catalyst-substrate adduct to be a genuine intermediate on the productive cycle toward catalysis. The influence of HOBt as an additive upon the reaction, catalyst resting state, and turnover-rate limiting step has been examined. Crossover experiments have probed the reversibility of each of the proposed steps of the catalytic cycle. Computations were also used to elucidate the origins of stereocontrol, with a 1,5-S···O interaction and the catalyst stereodirecting group providing transition structure rigidification and enantioselectivity, while preference for cation-π interactions over C-H···π is responsible for diastereoselectivity.
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Project description:As a significant type of cerebral cortical convolution pattern, the gyrus is widely preserved across species. Although many hypotheses have been proposed to study the underlying mechanisms of gyrus formation, it is currently still far from clear which factors contribute to the regulation of consistent gyrus formation. In this paper, we employ a joint analysis scheme of experimental data and computational modeling to investigate the fundamental mechanism of gyrus formation. Experimental data on mature human brains and fetal brains show that thicker cortices are consistently found in gyral regions and gyral cortices have higher growth rates. We hypothesize that gyral convolution patterns might stem from heterogeneous regional growth in the cortex. Our computational simulations show that gyral convex patterns may occur in locations where the cortical plate grows faster than the cortex of the brain. Global differential growth can only produce a random gyrification pattern, but it cannot guarantee gyrus formation at certain locations. Based on extensive computational modeling and simulations, it is suggested that a special area in the cerebral cortex with a relatively faster growth speed could consistently engender gyri.
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Project description:The purpose of this work was to investigate the effect of multifunctionality on material properties of synthetic polymer aerogels. For this purpose, we present the synthesis and characterization of monolithic dendritic-type urethane-acrylate monomers based on an aliphatic/flexible (Desmodur N3300), or an aromatic/rigid (Desmodur RE) triisocyanate core. The terminal acrylate groups (three at the tip of each of the three branches, nine in total) were polymerized with 2,2'-azobis(isobutyronitrile) (AIBN) via free radical chemistry. The resulting wet-gels were dried with supercritical fluid (SCF) CO₂. Aerogels were characterized with ATR-FTIR and solid-state 13C NMR. The porous network was probed with N₂-sorption and scanning electron microscopy (SEM). The thermal stability of aerogels was studied with thermogravimetric analysis (TGA). Most aerogels were macroporous materials (porosity > 80%), with high thermal stability (up to 300 °C). Aerogels were softer at low monomer concentrations and more rigid at higher concentrations. The material properties were compared with those of analogous aerogels bearing only one acrylate moiety at the tip of each branch and the same cores, and with those of analogous aerogels bearing norbornene instead of acrylate moieties. The nine-terminal acrylate-based monomers of this study caused rapid decrease of the solubility of the growing polymer and made possible aerogels with much smaller particles and much higher surface areas. For the first time, aliphatic/flexible triisocyanate-based materials could be made with similar properties in terms of particle size and surface areas to their aromatic/rigid analogues. Finally, it was found that with monomers with a high number of crosslinkable groups, material properties are determined by multifunctionality and thus aerogels based on 9-acrylate- and 9-norbornene-terminated monomers were similar. Materials with aromatic cores are carbonizable with satisfactory yields (20⁻30% w/w) to mostly microporous materials (BET surface areas: 640⁻740 m² g-1; micropore surface areas: 360⁻430 m² g-1).
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