Theoretical investigation into competing unimolecular reactions encountered in the pyrolysis of acetamide

Motivated by the necessity to understand the pyrolysis of alkylated amines, unimolecular decomposition of acetamide is investigated herein as a model compound. Standard heats of formation, entropies, and heat capacities, are calculated for all products and transition structures using several accurate theoretical levels. The potential energy surface is mapped out for all possible channels encountered in the pyrolysis of acetamide. The formation of acetamedic acid and 1-aminoethenol and their subsequent decomposition pathways are found to afford the two most energetically favored pathways. However, RRKM analysis shows that the fate of acetamedic acid and 1-aminoethenol at all temperatures and pressures is to reisomerize to the parent acetamide. 1-Aminoethenol, in particular, is predicted to be a long-lived species enabling its participation in bimolecular reactions that lead to the formation of the major experimental products. Results presented herein reflect the importance of bimolecular reactions involving acetamide and 1-aminoethenol in building a robust model for the pyrolysis of N-alkylated amides.     

Reactivity of the anti-Criegee intermediate of β-pinene with prevalent atmospheric species

Structural Chemistry - The reaction of the anti-Criegee intermediate (anti-CI) of β-pinene with prevalent atmospheric species has been investigated using quantum-chemical calculations. The...     

Computational study of the deamination reaction of cytosine with H2O and OH-

The mechanism for the deamination reaction of cytosine with H(2)O and OH(-) to produce uracil was investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels and for anions at the B3LYP/6-31+G(d) level. Single-point energies were also determined at B3LYP/6-31+G(d), MP2/GTMP2Large, and G3MP2 levels of theory. Thermodynamic properties (DeltaE, DeltaH, and DeltaG), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway that was investigated. Intrinsic reaction coordinate analysis was performed to characterize the transition states on the potential energy surface. Two pathways for deamination with H(2)O were found, a five-step mechanism (pathway A) and a two-step mechanism (pathway B). The activation energy for the rate-determining steps, the formation of the tetrahedral intermediate for pathway A and the formation of the uracil tautomer for pathway B, are 221.3 and 260.3 kJ/mol, respectively, at the G3MP2 level of theory. The deamination reaction by either pathway is therefore unlikely because of the high barriers that are involved. Two pathways for deamination with OH(-) were also found, and both of them are five-step mechanisms. Pathways C and D produce an initial tetrahedral intermediate by adding H(2)O to deprotonated cytosine which then undergoes three conformational changes. The final intermediate dissociates to product via a 1-3 proton shift. Deamination with OH(-), through pathway C, resulted in the lowest activation energy, 148.0 kJ/mol, at the G3MP2 level of theory.     

Mechanisms for the deamination reaction of cytosine with H2O/OH(-) and 2H2O/OH(-): a computational study

Mechanisms for the deamination reaction of cytosine with H 2O/OH (-) and 2H 2O/OH (-) to produce uracil were investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at MP2 and B3LYP using the 6-31G(d) basis set and at B3LYP/6-31+G(d) levels of theory. Single point energies were also determined at MP2/G3MP2Large and G3MP2 levels of theory. Thermodynamic properties (Delta E, Delta H, and Delta G), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway investigated. Intrinsic reaction coordinate (IRC) analysis was performed to characterize the transition states on the potential energy surface. Seven pathways for the deamination reaction were found. All pathways produce an initial tetrahedral intermediate followed by several conformational changes. The final intermediate for all pathways dissociates to product via a 1-3 proton shift. The activation energy for the rate-determining step, the formation of the tetrahedral intermediate for pathway D, the only pathway that can lead to uracil, is 115.3 kJ mol (-1) at the G3MP2 level of theory, in excellent agreement with the experimental value (117 +/- 4 kJ mol (-1)).     

A computational mechanistic study of the deamination reaction of melamine

A detailed computational study of the deamination reaction of melamine by OH^–, n H₂O/OH^–, n H₂O (where n = 1, 2, 3), and protonated melamine with H₂O, has been carried out using density functional theory and ab initio calculations. All structures were optimized at M06/6‐31G(d) level of theory, as well as with the B3LYP functional with each of the basis sets: 6‐31G(d), 6‐31 + G(d), 6‐31G(2df,p), and 6‐311++G(3df,3pd). B3LYP, M06, and ω B97XD calculations with 6‐31 + G(d,p) have also been performed. All structures were optimized at B3LYP/6‐31 + G(d,p) level of theory for deamination simulations in an aqueous medium, using both the polarizable continuum solvation model and the solvation model based on solute electron density. Composite method calculations have been conducted at G4MP2 and CBS‐QB3. Fifteen different mechanistic pathways were explored. Most pathways consisted of two key steps: formation of a tetrahedral intermediate and in the final step, an intermediate that dissociates to products via a 1,3‐proton shift. The lowest overall activation energy, 111 kJ mol^?1 at G4MP2, was obtained for the deamination of melamine with 3H₂O/OH^?.     

Exploring the potential of fluoro-flavonoid derivatives as anti-lung cancer agents: DFT,molecular docking,and molecular dynamics techniques

The present investigation utilized in silico methodologies to explore the diverse pharmacological activities, toxicity profiles, and chemical reactivity of a series of fluoro-flavonoid compounds ( 1 – 14 ), which are secondary metabolites of plants known for their broad range of biological effects. A comprehensive strategy is utilized, incorporating methods such as prediction of activity spectra for substances (PASS) prediction, absorption, distribution, metabolism, excretion, and toxicity (ADMET) assessments, and density functional theory (B3LYP) calculations using three basis sets: 6-31G(d,p), 6-311G(d,p), and 6-311++G(d,p). Furthermore, the study employed molecular docking technique to identify target proteins, including HER2 (7JXH), EGFR (4UV7), FPPS (1YQ7), HPGDS (1V40), DCK (1P60), and KEAP1 on Nrf2 (1X2J), for the investigated compounds, with cianidanol and genistein serving as reference drugs for the docking process. The investigated fluoro-flavonoid compounds exhibited significantly greater binding affinities (ranging from −8.3 to −10.6 kcal mol⁻¹) toward HER2, HPGDS, and KEAP1 compared to the reference drugs, cianidanol and genistein, which displayed binding affinities ranging from −8.4 to −9.4 kcal mol⁻¹. Furthermore, molecular dynamics simulations were conducted to assess the stability of the protein-ligand interaction, using the root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), Radius of gyration (Rg) parameters and principle component analysis (PCA). Among the tested fluoro-flavonoid analogs, analog 11 showed a RMSD value of .15 nm with the HER2 protein target, indicating a stable interaction. Based on in silico results, it appears that the fluoro-flavonoid compound 11 has the potential to serve as a targeted anti-lung cancer drug. However, additional in vivo and in vitro studies are necessary to confirm this hypothesis.     

The gas-phase ozonolysis reaction of methylbutenol: A mechanistic study

The gas-phase ozonolysis reaction of methylbutenol through the Criegee mechanism is investigated. The initial reaction leads to a primary ozonide (POZ) formation with barriers in the range of 10–28 kJ mol⁻¹. The formation of 2-hydroxy-2-methyl-propanal (HMP) and formaldehyde-oxide is more favorable, by 10 kJ mol⁻¹, than the syn-CI and formaldehyde. The unimolecular dissociation of the more stable syn-CI via 1,5-H transfer into an epoxide is more favored than the epoxide and ³O₂ formation. The ester channel led to the formation of the acetone and formic acid favorably from the anti-CI. The hydration of the anti-CI with H₂O and (H₂O)₂ is significantly barrierless with a higher plausibility to the latter, and thus they may lead to the formation of peroxides and ultimately OH radicals, as well as airborne particulate matter. Reaction of anti-CI with water dimers enhances its atmospheric reactivity by a factor of 28 in reference to water monomers.     

Mechanistic study of the deamination reaction of guanine: a computational study

The mechanism for the deamination of guanine with H(2)O, OH(-), H(2)O/OH(-) and for GuaH(+) with H(2)O has been investigated using ab initio calculations. Optimized geometries of the reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), B3LYP/6-31G(d), and B3LYP/6-31+G(d) levels of theory. Energies were also determined at G3MP2, G3MP2B3, G4MP2, and CBS-QB3 levels of theory. Intrinsic reaction coordinate (IRC) calculations were performed to characterize the transition states on the potential energy surface. Thermodynamic properties (ΔE, ΔH, and ΔG), activation energies, enthalpies, and Gibbs free energies of activation were also calculated for each reaction investigated. All pathways yield an initial tetrahedral intermediate and an intermediate in the last step that dissociates to products via a 1,3-proton shift. At the G3MP2 level of theory, deamination with OH(-) was found to have an activation energy barrier of 155 kJ mol(-1) compared to 187 kJ mol(-1) for the reaction with H(2)O and 243 kJ mol(-1) for GuaH(+) with H(2)O. The lowest overall activation energy, 144 kJ mol(-1) at the G3MP2 level, was obtained for the deamination of guanine with H(2)O/OH(-). Due to a lack of experimental results for guanine deamination, a comparison is made with those of cytosine, whose deamination reaction parallels that of guanine.     

Theoretical study on the unimolecular decomposition of thiophenol

The potential energy surface for the unimolecular decomposition of thiophenol (C(6)H(5)SH) is mapped out at two theoretical levels; BB1K/GTlarge and QCISD(T)/6-311+G(2d,p)//MP2/6-31G(d,p). Calculated reaction rate constants at the high pressure limit indicate that the major initial channel is the formation of C(6)H(6)S at all temperatures. Above 1000 K, the contribution from direct fission of the S-H bond becomes important. Other decomposition channels, including expulsion of H(2) and H(2)S are of negligible importance. The formation of C(6)H(6)S is predicted to be strong-pressure dependent above 900 K. Further decomposition of C(6)H(6)S produces CS and C(5)H(6). Overall, despite the significant difference in bond dissociation, i.e., 8-9 kcal/mol between the S-H bond in thiophenol and the O-H bond in phenol, H migration at the ortho position in the two molecules represents the most accessible initial channel.