Theoretical Study on the Kinetics of the Rubisco Carboxylase Reaction by a Model Based on Quantum Chemistry and Absolute Reaction Rate Theory.

The rate of the Rubisco carboxylase reaction is evaluated by statistical mechanics and hybrid density functional theory (DFT). The Rubisco molecular model given by Kannappan et al. was modified and used in the present calculation. The activation energies of CO2 addition reaction, H2O addition reaction, C2-C3 bond scission, and C2 protonation are estimated. We calculated the turnover number (TON) for each of the four reaction steps based on a revised absolute reaction rate theory, which became applicable to soft matter reactions. The molecular parameters used in TON calculations were obtained by DFT calculations. The TON of the total Rubisco reaction was finally evaluated using rate equations. The calculation in a vacuum gave the total TON to be around 5 × 10-5, which was much lower than the experimental value. The DFT calculation in water solvent gave the total TON to be around 0.1, which agreed reasonably well with experimentally reported values (∼2.71). The rate-limiting process was the scission reaction. The present calculation showed that both the phosphate groups in the substrate accelerate each reaction step. The present calculation showed that a more comprehensive molecular model including enolization and quantum chemical methods is necessary to make a more precise reaction model including the irreversibility of some reactions.

Spontaneous Combustion of 2-Bromo-3-Methoxythiophene: A Study on Reaction Pathways and Energetics by Quantum Chemical Calculations.

Reaction pathways and energetics for the dimerization and trimerization reactions of 2-bromo-3-methoxythiophene (2Br-3Met) molecules are investigated using hybrid density functional theory (DFT) calculations to obtain insight into the oligomerization reaction observed in the spontaneous combustion of pure liquid 2Br-3Met. The calculations show that the carbon-bromine bond in a 2Br-3Met molecule elongates easily, and the trans addition of this C-Br bond to a double bond in the neighboring 2Br-3Met molecule occurs easily at room temperature, reflecting the evaluated activation energy of ΔHa = 12.46 kcal/mol (enthalpy) or ΔGa = 35.68 kcal/mol (Gibbs free energy, 298.150 K and 1 atm). The formation process of trimers is calculated in a similar way. A model for the explanation of spontaneous combustion is proposed; large oligomers of the 2Br-3Met molecule are produced spontaneously following the initial formation of dimers or trimers. UV-vis spectra and vibration spectra are obtained for related molecular species, which show reasonable agreement with the experimental results.