A Coupled Reference Interaction Site Model/Molecular Dynamics Study of the Potential of Mean Force Curve of the SN2 Cl- + CH3Cl Reaction in Water

Theoretical estimation of kinetic parameters for nucleophilic substitution reactions in solution: an application of a solution translational entropy model

The kinetic parameters, such as activation entropy, activation enthalpy, activation free-energy, and reaction rate constant, for a series of nucleophilic substitution (SN) reactions in solution, are investigated using both a solution-phase translational entropy model and an ideal gas-phase translational entropy model. The results obtained from the solution translational entropy model are in excellent agreement with the experimental values, while the overestimation of activation free-energy from the ideal gas-phase translational entropy model is as large as 6.9 kcal mol(-1). For some of the reactions studied, such as and in methanol, and and in aqueous solution, the explicit + implicit model, namely, a cluster-continuum type model, should be employed to account for the strong solvent-solute interactions. In addition, the explicit + implicit models have also been applied to the DMSO-H2O mixtures, which would open up a door to investigate the reactions in a mixed solvent using density functional theory (DFT) methods.

Combined Electrostatically Embedded Multiconfiguration Molecular Mechanics and Molecular Mechanical Method: Application to Molecular Dynamics Simulation of a Chemical Reaction in Aqueous Solution with Hybrid Density Functional Theory

We here combine the electrostatically embedded multiconfiguration molecular mechanics (EE-MCMM) method for generating global potential energy surfaces in the presence of an electrostatic potential with molecular mechanics (MM). The resulting EE-MCMM/MM method is illustrated by applying it to carry out a molecular dynamics simulation for the symmetric bimolecular reaction Cl(-) + CH3Cl' → ClCH3 + Cl'(-) in aqueous solution with hybrid density functional theory as the quantum mechanical level. The potential of mean force is calculated, and the free energy barrier is found to be 25.3 kcal/mol, which is in good agreement with previous work. The advantage of the combined EE-MCMM and MM method is that the number of quantum mechanical calculations required for the active subsystem is very small compared to straight direct dynamics.

A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: multi-center molecular Ornstein-Zernike self-consistent field approach

In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl(-) + CH3Cl → ClCH3 + Cl(-)) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

Increasing the time step with mass scaling in Born-Oppenheimer ab initio QM/MM molecular dynamics simulations

Born-Oppenheimer ab initio QM/MM molecular dynamics simulation with umbrella sampling is a state-of-the-art approach to calculate free energy profiles of chemical reactions in complex systems. To further improve its computational efficiency, a mass-scaling method with the increased time step in MD simulations has been explored and tested. It is found that by increasing the hydrogen mass to 10 amu, a time step of 3 fs can be employed in ab initio QM/MM MD simulations. In all our three test cases, including two solution reactions and one enzyme reaction, the resulted reaction free energy profiles with 3 fs time step and mass scaling are found to be in excellent agreement with the corresponding simulation results using 1 fs time step and the normal mass. These results indicate that for Born-Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella sampling, the mass-scaling method can significantly reduce its computational cost while has little effect on the calculated free energy profiles.

Formalism for calculation of polymer-solvent-mediated potential

A simple theoretical approach is proposed for calculation of a solvent-mediated potential (SMP) between two colloid particles immersed in a polymer solvent bath in which the polymer is modeled as a chain with intramolecular degrees of freedom. The present recipe is only concerned with the estimation of the density profile of a polymer site around a single solute colloid particle instead of two solute colloid particles separated by a varying distance as done in existing calculational methods for polymer-SMP. Therefore the present recipe is far simpler for numerical implementation than the existing methods. The resultant predictions for the polymer-SMP and polymer solvent-mediated mean force (polymer-SMMF) are in very good agreement with available simulation data. With the present recipe, change tendencies of the contact value and second virial coefficiency of the SMP as a function of size ratio between the colloid particle and polymer site, the number of sites per chain, and the polymer concentration are investigated in detail. The metastable critical polymer concentration as a function of size ratio and the number of sites per chain is also reported for the first time. To yield the numerical solution of the present recipe at less than on a personal computer, a rapid and accurate algorithm for the numerical solution of the classical density functional theory is proposed to supply rapid and accurate estimation of the density profile of the polymer site as an input into the present formalism.

Carbon nanotube inner phase chemistry: the Cl- exchange SN2 reaction

Density functional calculations have been carried out to investigate the nature of the inner phase of a (6,6) carbon nanotube, using the Cl(-) exchange S(N)2 reaction as an indicator. Inside the carbon nanotube the classical barrier height increases by 6.6 kcal/mol due to the nanotube polarizability. This suggests that the inner phase environment can be considered a form of solid solvation, offering the possibility of obtaining altered guest properties and reactivity through dielectric stabilization.

Comparative Study on Solvation Free Energy Expressions in Reference Interaction Site Model Integral Equation Theory

The performance of the recently proposed partial wave (PW) free energy functional is compared with those of two previous expressions, Gaussian fluctuation (GF) and hypernetted chain (HNC), within the reference interaction site model framework. The applications to the calculations of ambient and supercritical water, solvation free energies of organic molecules, and partition coefficients clearly show that the PW and GF free energy expressions provide more reliable results than the HNC functional, indicating rather associative situations of geometry in ordinary liquids of medium-sized molecules.