Quantum mechanical and Rice-Ramsperger-Kassel-Marcus (RRKM) calculations are carried out to study the thermal unimolecular decomposition of oxetane (1), 2 methyloxetane (2), and 2,2 dimeth yloxetane (3) at the MPW1PW91/6 311 + G** level of theory. The results of the calculations reveal that decomposition reaction of compounds 1-3 yields formaldehyde and the corresponding substituted olefin. The predicted high pressure limit rate constants for the decomposition compounds 1-3 are represented as 6.61 × 10 13 exp(-32472/T), 9.33 × 10 13 exp(-29873/T), and 4.79 × 10 13 exp(-27055/T) s -1 , respectively. The fall off pressures for the decomposition of compounds 1-3 are found to be 9.42 × 10 -2 , 3.67 × 10 -3 , and 7.26 × 10 -4 mm Hg, respectively. As the fall off pressure of the decomposition process of compounds 1-3 are in the following order: P 1/2 (1) > P 1/2 (2) > P 1/2 (3); therefore the decomposition rates are as follow: rate(1) < rate(2) < rate(3).
Quantum mechanical and molecular dynamics methods were used to analyze the structure and stability of neutral and zwitterionic configurations of the extracted active site sequence from a Burkholderia cepacia lipase, histidyl-seryl-glutamin (His86-Ser87-Gln88) and its mutated form, histidyl-cysteyl-glutamin (His86-Cys87-Gln88) in vacuum and different solvents. The effects of solvent dielectric constant, explicit and implicit water molecules and side chain mutation on the structure and stability of this sequence in both neutral and zwitterionic forms are represented. The quantum mechanics computations represent that the relative stability of zwitterionic and neutral configurations depends on the solvent structure and its dielectric constant. Therefore, in vacuum and the considered non-polar solvents, the neutral form of the interested sequences is more stable than the zwitterionic form, while their zwitterionic form is more stable than the neutral form in the aqueous solution and the investigated polar solvents in most cases. However, on the potential energy surfaces calculated, there is a barrier to proton transfer from the positively charged ammonium group to the negatively charged carboxylat group or from the ammonium group to the adjacent carbonyl oxygen and or from side chain oxygen and sulfur to negatively charged carboxylat group. Molecular dynamics simulations (MD) were also performed by using periodic boundary conditions for the zwitterionic configuration of the hydrated molecules in a box of water molecules. The obtained results demonstrated that the presence of explicit water molecules provides the more compact structures of the studied molecules. These simulations also indicated that side chain mutation and replacement of sulfur with oxygen leads to reduction of molecular flexibility and packing.
Kinetic rate constants for the oxidation reaction of the hydroxyl radical with CH3SH, C2H5SH, n-C3H7SH, and iso-C3H7SH under inert (Ar) conditions over the temperature range 252–430 K have been studied theoretically using density functional theory along with various exchange–correlation functionals as well as the benchmark CBS-QB3 quantum chemical approach. Bimolecular rate constants were estimated using transition state theory and the statistical Rice–Ramsperger–Kassel–Marcus theory. Comparison with experiment confirms that in the OH addition reaction pathways leading to the related products, the first bimolecular reaction steps have effective negative activation energy barriers. Effective rate constants have been calculated according to a steady-state analysis of a two-step model reaction mechanism. As a consequence of the negative activation energies, pressures higher than 104 bar are required to reach the high-pressure limit. Both from thermodynamic and kinetic viewpoints, the most favorable process here is the oxidation reaction of hydroxyl radicals with n-C3H7SH.
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