Theoretical investigations have been carried out on the mechanism and kinetics for the reaction of CF 3 CHO + Cl using duallevel direct dynamics method. The potential energy surface information was obtained at the MCQCISD/3//MP2/cc-pVDZ level and the kinetic calculations were done using variational transition state theory with interpolated single-point energy (VTST-ISPE) approach. The calculated results show that the reaction proceeds primarily via the H-abstraction channel, while the Cl-addition channel is unfavorable due to the higher barriers. The improved canonical variational transition-state theory (ICVT) with the small-curvature tunneling correction (SCT) was used to calculate the rate constants. The theoretical rate constants at room temperature are in general agreement with the experimental values. A three-parameter rate constant expression was fitted over a wide temperature range of 200-2000 K.
Phosphonylation and aging processes between butyrylcholinesterase with mipafox have been studied at the B3LYP/6-311G(d,p) level of theory. The calculated results indicate that the phosphonylation process employs a two-step addition-elimination mechanism with the addition (the first step) as the rate-limiting step. Two different calculation models revealed that the catalytic triad of butyrylcholinesterase plays an important role in accelerating the reaction. This is the same mechanism as the phosphonylation reaction of acetylcholinesterase by sarin reported by Wang et al. However, the energy barrier of the rate-limiting step in the present reaction is higher than that in phosphonylation reaction of acetylcholinesterase by sarin. This indicates the differences in the phosphonylation activity of sarin and mipafox. The aging process occurs through a two-step addition-elimination mechanism similar to the phosphonylation process with the addition as the rate-limiting step. The solvent effects have been evaluated by using a CPCM model and the results show that the stationary structures and the negative charges around some important atoms involved in the two processes are not significantly different. However, the energy barrier of the phosphonylation process is remarkably decreased, revealing that this process is feasible in solution.
In this work,we developed the CHARMM all-atom force field parameters for the nonstandard biological residue chalcone,followed by the standard protocol for the CHARMM27 force field development.Target data were generated via ab initio calculations at the MP2/6-31G* and HF/6-31G* levels.The reference data included interaction energies between water and the model compound F(a fragment of chalcone).Bond,angle,and torsion parameters were derived from the ab initio calculations and renormalized to maintain compatibility with the existing CHARMM27 parameters of standard residues.The optimized CHARMM parameters perform well in reproducing the target data.We expect that the extension of the CHARMM27 force field parameters for chalcone will facilitate the molecular simulation studies of the reaction mechanism of intramolecular cyclization of chalcone catalyzed by chalcone isomerase.
