Dunyou Wang

Hybrid Quantum Mechanical/Molecular Mechanics Study of the SN2 Reaction of CH3Cl+OH– in Water

The S(N)2 mechanism for the reaction of CH(3)Cl + OH(-) in aqueous solution was investigated using combined quantum mechanical and molecular mechanics methodology. We analyzed structures of reactant, transition, and product states along the reaction pathway. The free energy profile was calculated using the multilayered representation with the DFT and CCSD(T) level of theory for the quantum-mechanical description of the reactive region. Our results show that the aqueous environment has a significant impact on the reaction process. We find that solvation energy contribution raises the reaction barrier by ~18.9 kcal/mol and the reaction free energy by ~24.5 kcal/mol. The presence of the solvent also induces perturbations in the electronic structure of the solute leading to an increase of 3.5 kcal/mol for the reaction barrier and a decrease of 5.6 kcal/mol for the reaction free energy, respectively. Combining the results of two previous calculation results on CHCl(3) + OH(-) and CH(2)Cl(2) + OH(-) reactions in water, we demonstrate that increase in the chlorination of the methyl group (from CH(3)Cl to CHCl(3)) is accompanied by the decrease in the free energy reaction barrier, with the CH(3)Cl + OH(-) having the largest barrier among the three reactions.

Hybrid Quantum Mechanical and Molecular Mechanics Study of the SN2 Reaction of CCl4 + OH– in Aqueous Solution: The Potential of Mean Force, Reaction Energetics, and Rate Constants

The bimolecular nucleophilic substitution reaction of CCl(4) and OH(-) in aqueous solution was investigated on the basis of a combined quantum mechanical and molecular mechanics method. A multilayered representation approach is employed to achieve high accuracy results at the CCSD(T) level of theory. The potential of mean force calculations at the DFT level and CCSD(T) level of theory yield reaction barrier heights of 22.7 and 27.9 kcal/mol, respectively. Both the solvation effects and the solvent-induced polarization effect have significant contributions to the reaction energetics, for example, the solvation effect raises the saddle point by 10.6 kcal/mol. The calculated rate constant coefficient is 8.6 × 10(-28) cm(3) molecule(-1) s(-1) at the standard state condition, which is about 17 orders magnitude smaller than that in the gas phase. Among the four chloromethanes (CH(3)Cl, CH(2)Cl(2), CHCl(3), and CCl(4)), CCl(4) has the lowest free energy activation barrier for the reaction with OH(-) in aqueous solution, confirming the trend that substitution of Cl by H in chloromethanes diminishes the reactivity.

Quantum Dynamics Study of Vibrational Excitation Effects and Energy Requirement on Reactivity for the O + CD4/CHD3 → OD/OH + CD3 Reactions

A quantum reactive dynamics, six-degrees-of-freedom, time-dependent wave packet method is employed to study vibrational enhancement and energy requirement on reactivity of the O((3)P) + CD4/CHD3 → OD/OH + CD3 reactions. The calculations show, for O + CD4, that all the vibrational excitations of CD4 enhance reactivity, which agrees with quasi-classical trajectory results. However, this finding contradicts the experimental observation where the bending excitation suppresses reactivity. The present study also reveals that translational energy, in general, is more effective to enhance reactivity than vibrational energy; however, at higher collision energy, vibrational energy is slightly more effective than translational energy. For O + CHD3, the stretching and bending excitations of CHD3 enhance the reaction, whereas the umbrella motion hinders reactivity. The calculated excitation functions agree well with experiments.

CH2Cl2 + OH- reaction in aqueous solution: a combined quantum mechanical and molecular mechanics study.

The CH2Cl2 + OH(-) reaction in aqueous solution was investigated using combined quantum mechanical and molecular mechanics approach. We present analysis of the reactant, transition, and product state structures and calculate the free energy reaction profile through the CCSD(T) level of the theory for the reactive region. Our results show that the aqueous environment has a significant impact on the reaction process, raising the reaction barrier by ∼ 17 kcal/mol and the reaction energy by ∼ 20 kcal/mol. While solvation effects play a predominant role, we also find sizable contributions from solvent-induced polarization effects.

Catalytic Effect of Aqueous Solution in Water-Assisted Proton Transfer Mechanism of 8-hydroxy Guanine Radical

Water-assisted proton-transfer process is a key step in guanine damage reaction by hydroxyl radical in aqueous solution. In this article, we quantitatively determine the solvent effect in water-assisted proton-transfer mechanism of 8-hydroxy guanine radical using combined quantum mechanics and molecular mechanism with an explicit solvation model. Atomic-level reaction pathway was mapped, which shows a synchronized two-proton-transfer mechanism between the assistant water molecule and 8-hydroxy guanine radical. The transition-state dipole moment is the largest along the reaction pathway, which electrostatically stabilizes the proton-transfer transition-state complex. The free-energy reaction barrier for this water-assisted proton-transfer reaction was calculated at 19.2 kcal/mol with the density functional theory/M08-SO/cc-pVTZ+/molecular mechanics level of theory. The solvent effect not only has a big impact on geometries, but also dramatically changes the energetics along the reaction pathway. Among the solvent effect contributions to the transition state, the solvent energy contribution is -28.5 kcal/mol and the polarization effect contribution is 19.9 kcal/mol. In total, the solvent effect contributes -8.6 kcal/mol to the free-energy barrier height, which means that the presence of aqueous solution has a catalytic effect on the reaction mechanism and enhances the proton-transfer reactivity in aqueous solution.

Multilevel Quantum Mechanics Theories and Molecular Mechanics Calculations of the Cl– + CH3I Reaction in Water

The Cl- + CH3I → CH3Cl + I- reaction in water was studied using combined multilevel quantum mechanism theories and molecular mechanics with an explicit water solvent model. The study shows a significant influence of aqueous solution on the structures of the stationary points along the reaction pathway. A detailed, atomic-level evolution of the reaction mechanism shows a concerted one-bond-broken and one-bond-formed mechanism, as well as a synchronized charge-transfer process. The potentials of mean force calculated with the CCSD(T) and DFT treatments of the solute produce a free activation barrier at 24.5 and 19.0 kcal/mol, respectively, which agrees with the experimental one at 22.0 kcal/mol. The solvent effects have also been quantitatively analyzed: in total, the solvent effects raise the activation energy by 20.2 kcal/mol, which shows a significant impact on this reaction in water.