Theoretical Study of the Mechanism for the Reaction of Trimethylaluminum with Ozone
Ontology highlight
ABSTRACT:
SUBMITTER: Kayanuma M
PROVIDER: S-EPMC8515592 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Density functional theory calculations are used to investigate the detailed reaction mechanism of benzoylformate decarboxylase, a thiamin diphosphate (ThDP)-dependent enzyme that catalyzes the nonoxidative decarboxylation of benzoylformate yielding benzaldehyde and carbon dioxide. A large model of the active site is constructed on the basis of the X-ray structure, and it is used to characterize the involved intermediates and transition states and evaluate their energies. There is generally good agreement between the calculations and available experimental data. The roles of the various active site residues are discussed and the results are compared to mutagenesis experiments. Importantly, the calculations identify off-cycle intermediate species of the ThDP cofactor that can have implications on the kinetics of the reaction.
| S-EPMC6028569 | biostudies-literature
Project description:Theoretical investigations are performed on mechanism and kinetics of the reaction of halogen peroxy radical ClOO with NO radical. The electronic structure information for both of the singlet and triplet potential energy surfaces (PESs) is obtained at the MP2/6-311 + G(2df) level of theory, and the single-point energies are refined by the CCSD(T)/6-311 + G(2df) level. The rate constants for various product channels of the reaction in the pressure range of 1-7600 Torr are predicted. The main results are as follows: On the singlet surface, the addition-elimination mechanism is the most important. First, the N atom of the NO radical can attack the O atom of the ClOO radical to form an energy-riched intermediate IM1 ClOONOtp (21.3 kcal/mol) barrierlessly, then IM1 could isomerizes to IM2 ClOONOcp (22.1 kcal/mol) via a low energy barrier. Both IM1 and IM2 can dissociate to the primary product P? ClNO + ¹O? and the secondary product P? ClO + NO?. On the triplet surface, the direct Cl-abstraction reaction is the most feasible pathway. The Cl-abstraction can take place via a van der Waals complex, ³IM1 ONClOO (4.1 kcal/mol), then it fragments readily to give P?' ClNO + ³O? with a small barrier. The kinetic calculations show that at low temperatures, the singlet bimolecular product P? is the primary product, while at high temperatures, the triplet product P?' becomes the primary one; only at high pressures and low temperatures, the unimolecular products IM1 and IM2 can be found with quite small yields. At experimentally measured temperature 213 K, ClNO is the primary product in the whole pressure range, which is consistent with the previous experiment. The present study may be useful for further experimental studies for the title reaction.
| S-EPMC6149737 | biostudies-other
Project description:The reaction mechanism of cis-3-chloroacrylic acid dehalogenase (cis-CaaD) is studied using the B3LYP density functional theory method. This enzyme catalyzes the hydrolytic dehalogenation of cis-3-chloroacrylic acid to yield malonate semialdehyde and HCl. The uncatalyzed reaction is first considered, and excellent agreement is found between the calculated barrier and the measured rate constant. The enzymatic reaction is then studied with an active site model consisting of 159 atoms. The results suggest an alternative mechanism for cis-CaaD catalysis and different roles for some active site residues in this mechanism.
| S-EPMC2798121 | biostudies-literature
Project description:Using density functional theory and a cluster approach, we study the reaction potential surface and compute Gibbs free energies for the acylate reaction of β-lactamase with penicillin G, where the solvent effect is important and taken into consideration. Two reaction paths are investigated: one is a multi-step process with a rate-limit energy barrier of 19.1 kcal/mol, which is relatively small, and the reaction can easily occur; the other is a one-step process with a barrier of 45.0 kcal/mol, which is large and thus makes the reaction hard to occur. The reason why the two paths have different barriers is explained.
| S-EPMC8154126 | biostudies-literature
Project description:We present an Al2O3 dielectric layer on molybdenum disulfide (MoS2), deposited using atomic layer deposition (ALD) with ozone/trimethylaluminum (TMA) and water/TMA as precursors. The results of atomic force microscopy and low-energy ion scattering spectroscopy show that using TMA and ozone as precursors leads to the formation of uniform Al2O3 layers, in contrast to the incomplete coverage we observe when using TMA/H2O as precursors. Our Raman and X-ray photoelectron spectroscopy measurements indicate minimal variations in the MoS2 structure after ozone treatment at 200 °C, suggesting its excellent chemical resistance to ozone.
| S-EPMC4134179 | biostudies-literature
Project description:The mechanism and kinetics underlying reactions between the naturally-occurring antioxidant sinapic acid (SA) and the very damaging ·NO2 and ·OH were investigated through the density functional theory (DFT). Two most possible reaction mechanisms were studied: hydrogen atom transfer (HAT) and radical adduct formation (RAF). Different reaction channels of neutral and anionic sinapic acid (SA-) scavenging radicals in both atmosphere and water medium were traced independently, and the thermodynamic and kinetic parameters were calculated. We find the most active site of SA/SA- scavenging ·NO2 and ·OH is the -OH group in benzene ring by HAT mechanism, while the RAF mechanism for SA/SA- scavenging ·NO2 seems thermodynamically unfavorable. In water phase, at 298 K, the total rate constants of SA eliminating ·NO2 and ·OH are 1.30×108 and 9.20×109 M-1 S-1 respectively, indicating that sinapic acid is an efficient scavenger for both ·NO2 and ·OH.
| S-EPMC5021273 | biostudies-literature
Project description:A detailed knowledge of the reactivity of 2,3,7,8-tetrachlorodibenzofuran (TCDF) at the molecular level is important to better understand the transformation of dioxins analogous to TCDF in the environment. To clarify the reactivity of the organic hydroperoxides toward TCDF, the reaction of the TCDF with hydrogen peroxide (H2O2) and its anion has been investigated theoretically. For the reaction of the neutral H2O2, a molecular complex can be formed between TCDF and H2O2 first. Then, the nucleophilic aromatic substitution of TCDF by H2O2 occurs in the presence of the water molecules to form an intermediate containing an O-O bond. Finally, the O-O bond cleavages homolytically for the above intermediate. On the other hand, as for the reaction of the anion of H2O2 (HO2 -), the nucleophilic addition of HO2 - to TCDF can also occur besides the nucleophilic aromatic substitution reaction mentioned above, resulting in the dissociation of the C-O bond of TCDF. Unlike the reaction involving neutral H2O2, no water molecules are required. In addition, the selected substitution effects, such as F-, Br-, and CH3-substituents, on the reactivity of the above reaction have also been explored. Hopefully, the present results can enable us to gain insights into the reactivity of the organic hydroperoxides with TCDF-like environmental pollutants.
| S-EPMC6648065 | biostudies-literature
Project description:The biogenetic origin of triterpene dimers from the Celastraceae family has been proposed as assisted hetero-Diels-Alder reaction (HDA). In this work, computational calculation of HDA between natural quinonemethides (tingenone and isopristimerol) and hypothetical orthoquinones has been performed at the M06-2X/6-31G(d) level of theory. We have located all the HDA transition states supporting the biogenetic route via HDA cycloadditions. We found that all reactions take place through a concerted inverse electron demand and asynchronous mechanism. The enzymatic assistance for dimer formation was analyzed in terms of the calculated transition state energy barrier.
| S-EPMC6273858 | biostudies-other
Project description:The C-C bond cleavage catalyzed by metal-dependent iso-orotate decarboxylase (IDCase) from the thymidine salvage pathway is of interest for the elucidation of a (hypothetical) DNA demethylation pathway. IDCase appears also as a promising candidate for the synthetic regioselective carboxylation of N-heteroaromatics. Herein, we report a joint experimental-theoretical study to gain insights into the metal identity, reaction mechanism, and substrate specificity of IDCase. In contrast to previous assumptions, the enzyme is demonstrated by ICPMS/MS measurements to contain a catalytically relevant Mn2+ rather than Zn2+. Quantum chemical calculations revealed that decarboxylation of the natural substrate (5-carboxyuracil) proceeds via a (reverse) electrophilic aromatic substitution with formation of CO2. The occurrence of previously proposed tetrahedral carboxylate intermediates with concomitant formation of HCO 3 - could be ruled out on the basis of prohibitively high energy barriers. In contrast to related o-benzoic acid decarboxylases, such as γ-resorcylate decarboxylase and 5-carboxyvanillate decarboxylase, which exhibit a relaxed substrate tolerance for phenolic acids, IDCase shows high substrate fidelity. Structural and energy comparisons suggest that this is caused by a unique hydrogen bonding of the heterocyclic natural substrate (5-carboxyuracil) to the surrounding residues. Analysis of calculated energies also shows that the reverse carboxylation of uracil is impeded by a strongly disfavored uphill reaction.
| S-EPMC6305744 | biostudies-literature
Project description:The mechanism of the phenol-epoxide ring-opening reaction using tetraphenylphosphonium-tetraphenylborate (TPP-K) was investigated using the density functional theory (DFT) method. The reaction was initiated by breaking the P-B bond of TPP-K. The generated tetraphenylborate (TetraPB-) reacted with phenol to form a phenoxide ion, which combined with tetraphenylphosphonium (TPP+) to produce the active species, i.e., tetraphenylphosphonium phenolate (TPP-OPh). The phenoxide ion in TPP-OPh nucleophilically attacked the epoxide. Simultaneously, the H atom in the phenolic OH group moved to the O atom of the ring-opened epoxide. The formed phenoxide ion bound to TPP+ again, and TPP-OPh was regenerated. The rate-determining steps in the reaction were the cleavage of the P-B bond and the triphenylborane-forming reaction. The free energies of activation were calculated to be 36.3 and 36.1 kcal/mol, respectively. It is also suggested that these values in the rate-determining steps could be manipulated by substituents introduced on the Ph group of TetraPB-. Based on these results, it is possible to construct new design guidelines for latent hardening accelerators such as TPP-K.
| S-EPMC9861531 | biostudies-literature