Quantum calculation method has been used to understand and investigate the free radical reactions of propane with hydroxyl radical in vacuum through modem quantum mechanics that is package on hyperchem 8.02 program. O...Quantum calculation method has been used to understand and investigate the free radical reactions of propane with hydroxyl radical in vacuum through modem quantum mechanics that is package on hyperchem 8.02 program. Optimized structures and structural reactivates have been studied through bond stability and angles using DFT calculation based on the basis set 6-31G＊. Energetic properties have been calculated like total energy, Gibbs free energy, entropy, heat of formation, and rate constant for all chemical species that＇s participate in the suggested reaction mechanism. Reaction mechanism and rate determining step had been suggested according to calculation of energy barrier values, and compares between the suggested competitive reactions for each probable reaction step. Suggested structures and the probable transition states have been studied.展开更多
The scaling behaviors of the nucleon resonance transition amplitudes from perturbative QCD (PQCD) are utilized to parametrize the amplitudes of the first negative-parity nucleon resonance . Our analysis indicates that...The scaling behaviors of the nucleon resonance transition amplitudes from perturbative QCD (PQCD) are utilized to parametrize the amplitudes of the first negative-parity nucleon resonance . Our analysis indicates that the constraints of the transition amplitude for the resonance at the limit by QCD sum rule calculations are not applicable at a moderate range of compared with the present available data if the contribution of is dominant in the limit.展开更多
The mechanism of the nucleotidyl transfer reaction catalyzed by yeast RNA polymerase I1 has been investigated using molec- ular mechanics and quantum mechanics methods. Molecular dynamics （MD） simulations were carri...The mechanism of the nucleotidyl transfer reaction catalyzed by yeast RNA polymerase I1 has been investigated using molec- ular mechanics and quantum mechanics methods. Molecular dynamics （MD） simulations were carried out using the TIP3 water model and generalized solvent boundary potential （GSBP） by CHARMM based on the X-ray crystal structure. Two models of the ternary elongation complex were constructed based on CHARMM MD calculations. All the species including reactants, transition states, intermediates, and products were optimized using the DFT-PBE method coupled with the basis set DZVP and the auxiliary basis set GEN-A2. Three pathways were explored using the DFT method. The most favorable reaction pathway involves indirect proton migration from the RNA primer 3＇-OH to the oxygen atom of a-phosphate via a solvent water mole- cule, proton rotation from the oxygen atom of a-phosphate to the 13-phosphate side, the RNA primer 3＇-O nucleophilic attack on the a-phosphorus atom, and P-O bond breakage. The corresponding reaction potential profile was obtained. The rate limit- ing step, with a barrier height of 21.5 kcal/mol, is the RNA primer 3＇-0 nucleophilic attack, rather than the commonly consid- ered proton transfer process. A high-resolution crystal structure including crystallographic water molecules is required for fur- ther studies.展开更多
文摘Quantum calculation method has been used to understand and investigate the free radical reactions of propane with hydroxyl radical in vacuum through modem quantum mechanics that is package on hyperchem 8.02 program. Optimized structures and structural reactivates have been studied through bond stability and angles using DFT calculation based on the basis set 6-31G＊. Energetic properties have been calculated like total energy, Gibbs free energy, entropy, heat of formation, and rate constant for all chemical species that＇s participate in the suggested reaction mechanism. Reaction mechanism and rate determining step had been suggested according to calculation of energy barrier values, and compares between the suggested competitive reactions for each probable reaction step. Suggested structures and the probable transition states have been studied.
文摘The scaling behaviors of the nucleon resonance transition amplitudes from perturbative QCD (PQCD) are utilized to parametrize the amplitudes of the first negative-parity nucleon resonance . Our analysis indicates that the constraints of the transition amplitude for the resonance at the limit by QCD sum rule calculations are not applicable at a moderate range of compared with the present available data if the contribution of is dominant in the limit.
基金supported by the Natural Sciences and Engineering Research Council of Canada (10174)the Project-sponsored by SRF for ROCS,SEM
文摘The mechanism of the nucleotidyl transfer reaction catalyzed by yeast RNA polymerase I1 has been investigated using molec- ular mechanics and quantum mechanics methods. Molecular dynamics （MD） simulations were carried out using the TIP3 water model and generalized solvent boundary potential （GSBP） by CHARMM based on the X-ray crystal structure. Two models of the ternary elongation complex were constructed based on CHARMM MD calculations. All the species including reactants, transition states, intermediates, and products were optimized using the DFT-PBE method coupled with the basis set DZVP and the auxiliary basis set GEN-A2. Three pathways were explored using the DFT method. The most favorable reaction pathway involves indirect proton migration from the RNA primer 3＇-OH to the oxygen atom of a-phosphate via a solvent water mole- cule, proton rotation from the oxygen atom of a-phosphate to the 13-phosphate side, the RNA primer 3＇-O nucleophilic attack on the a-phosphorus atom, and P-O bond breakage. The corresponding reaction potential profile was obtained. The rate limit- ing step, with a barrier height of 21.5 kcal/mol, is the RNA primer 3＇-0 nucleophilic attack, rather than the commonly consid- ered proton transfer process. A high-resolution crystal structure including crystallographic water molecules is required for fur- ther studies.
