Two-dimensional free-energy surface on the exchange reaction of alkyl chloride/chloride using the QM/MM-MC method

Ohisa, Masayuki; Yamataka, Hiroshi; Dupuis, Michel; Aida, Misako

doi:10.1039/b712565h

Cited by 6 publications

(6 citation statements)

References 18 publications

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“…This map makes it possible to locate the transition structures of the reaction in solution. There have been continuing efforts to obtain TS structures in solution 24–26. Hu et al27 developed a methodology of QM/MM minimum free‐energy path and applied it to a protein reaction.…”

Section: Methods Of Calculationsmentioning

confidence: 99%

A free‐energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): Application to highly solvent‐dependent reactions

et al. 2010

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This study describes the framework of the quantum mechanical (QM)/Monte Carlo (MC)/free-energy perturbation (FEP) method, a FEP method based on MC simulations using quantum chemical calculations. Because a series of structures generated by interpolating internal coordinates between transition state and reactant did not produce smooth free-energy profiles, we used structures from the intrinsic reaction coordinate calculations. This method was first applied to the Diels-Alder reaction between methyl vinyl ketone and cyclopentadiene and produced ΔG( sol)‡ values of 20.1 and 21.4 kcal mol(-1) in aqueous and methanol solutions, respectively. They are very consistent with the experimentally observed values. The other two applications were the free-energy surfaces for the Cope elimination of N,N-dimethyl-3-phenylbutan-2-amine oxide in aqueous, dimethyl sulfoxide, and tetrahydrofuran solutions, and the Kemp decarboxylation of 6-hydroxybenzo-isoxazole-3-carboxylic acid in aqueous, dimethyl sulfoxide, and CH(3) CN solutions. The calculated activation free energies differed by less than 1.8 kcal mol(-1) from the experimental values for these reactions. Although we used droplet models for the QM/MC/FEP simulations, the calculated results for three reactions are very close to the experimental data. It was confirmed that most of the interactions between the solute and solvents can be described using small numbers of solvent molecules. This is because a few solvent molecules can produce large portions of the solute-solvent interaction energies at the reaction centers. When we confirmed the dependency on the droplet sizes of solvents, the QM/MC/FEP for a large droplet with 106 water molecules produced a ΔG (sol)‡ value similar to the experimental values, as well as that for a small droplet with 34 molecules.

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Section: Methods Of Calculationsmentioning

confidence: 99%

A free‐energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): Application to highly solvent‐dependent reactions

et al. 2010

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“…It is now possible to calculate changes in the free energy for reactions in solution with a reasonable computational cost [1][2][3]. To understand the effect of solvation on the reactivities or properties of solute molecules, it is also important to elucidate the distribution of solvent molecules, i.e., the solvation pattern.…”

Section: Introductionmentioning

confidence: 99%

Solvent distributions, solvent orientations and specific hydration regions around 1-adamantyl chloride and adamantane in aqueous solution

Ohisa

Aida

2011

Chemical Physics Letters

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a b s t r a c tAb initio molecular orbital theory and Monte Carlo method with molecular mechanics are used to calculate the hydration numbers and solvent configurations around 1-adamantyl chloride in 324 water molecules. In the highest probability region for distribution of water molecules, a water molecule forms two hydrogen bonds with Cl and the adamantane skeleton; in the second highest probability region, a water molecule is located at the rear side. The CHÁ Á ÁO interaction in the rear side is enhanced by the Cl substitution. The water orientation in the rear side of 1-adamantyl chloride is different from that around a hydrophobic adamantane molecule.

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“…Thus, to achieve sufficient accuracy and allow extensive configurational sampling of these large systems, a multilevel treatment has to be applied. − A wide range of applications have been published, e.g. for condensed-phase reactions, − nanostructured materials, brittle fracture, and catalytic systems, such as zeolites or enzymes. , …”

Section: Introductionmentioning

confidence: 99%

Evaluating Boundary Dependent Errors in QM/MM Simulations

et al. 2009

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Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations provide a powerful tool for studying chemical reactions, especially in complex biochemical systems. In most works to date, the quantum region is kept fixed throughout the simulation and is defined in an ad hoc way based on chemical intuition and available computational resources. The simulation errors associated with a given choice of the quantum region are, however, rarely assessed in a systematic manner. Here we study the dependence of two relevant quantities on the QM region size: the force error at the center of the QM region and the free energy of a proton transfer reaction. Taking lysozyme as our model system, we find that in an apolar region the average force error rapidly decreases with increasing QM region size. In contrast, the average force error at the polar active site is considerably higher, exhibits large oscillations and decreases more slowly, and may not fall below acceptable limits even for a quantum region radius of 9.0 A. Although computation of free energies could only be afforded until 6.0 A, results were found to change considerably within these limits. These errors demonstrate that the results of QM/MM calculations are heavily affected by the definition of the QM region (not only its size), and a convergence test is proposed to be a part of setting up QM/MM simulations.

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Two-dimensional free-energy surface on the exchange reaction of alkyl chloride/chloride using the QM/MM-MC method

Cited by 6 publications

References 18 publications

A free‐energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): Application to highly solvent‐dependent reactions

A free‐energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): Application to highly solvent‐dependent reactions

Solvent distributions, solvent orientations and specific hydration regions around 1-adamantyl chloride and adamantane in aqueous solution

Evaluating Boundary Dependent Errors in QM/MM Simulations

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