A two-dimensional energy surface for a type II SN2 reaction in aqueous solution

Gao, Jiali; Xia, Xinfu

doi:10.1021/ja00074a036

Cited by 125 publications

(133 citation statements)

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“…41 The rest of the enzyme and/or water molecules form the MM subsystem described by means of the all-atoms Optimized Potential for Liquid Simulation (OPLS) for the enzyme 42 and a flexible TIP3P potential for water molecules. 43 The LenardJones parameters for the QM/MM interactions are also taken form the OPLS potential except for the chlorine atoms, for which we used those from ref 44 .…”

Section: Methodsmentioning

confidence: 99%

Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates

et al. 2013

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Section: Methodsmentioning

confidence: 99%

Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates

et al. 2013

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“…38,39 The Lennard-Jones parameters employed for the quantum atoms in the calculation of the dispersion-repulsion interaction between the quantum and classical subsystems were taken from Ref. 40. The molecular mechanics subsystem was described by means of the TIP3P potential.…”

Section: Methodsmentioning

confidence: 99%

A quantum mechanics-molecular mechanics study of dissociative electron transfer: The methylchloride radical anion in aqueous solution

Soriano

Silla

Tuñón

2002

The Journal of Chemical Physics

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The dissociative electron transfer reaction CH 3 Clϩe Ϫ →CH 3• ϩCl Ϫ in aqueous solution is studied by using a QM/MM method. In this work the quantum subsystem ͑a methylchloride molecule plus an electron͒ is described using density functional theory while the solvent ͑300 water molecules͒ is described using the TIP3P classical potential. By means of molecular dynamics simulations and the thermodynamic integration technique we obtained the potential of mean force ͑PMF͒ for the carbon-chlorine bond dissociation of the neutral and radical anion species. Combining these two free energy curves we found a quadratic dependence of the activation free energy on the reaction free energy in agreement with Marcus' relationship, originally developed for electron transfer processes not involving bond breaking. We also investigated dynamical aspects by means of 60 dissociative trajectories started with the addition of an extra electron to different configurations of a methylchloride molecule in solution. The PMF shows the existence of a very flat region, in which the system is trapped during some finite time if the quantum subsystem quickly losses its excess kinetic energy transferring it to the solvent molecules. One of the most important factors determining the effectiveness of this energy transfer seems to be the existence of close contacts ͑hydrogen bonds͒ between the solute and the solvent.

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“…[1][2][3] Conventional dual-resolution approaches 4,5 define the active region as a preselected set of atoms. This strategy works well if the molecular system is rigid, but in a solute-solvent system HR solvent molecules readily diffuse away from the active region, to be replaced by LR solvent molecules.…”

Section: Introductionmentioning

confidence: 99%

Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials

Boereboom

Potestio

Donadio

et al. 2016

J. Chem. Theory Comput.

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Adaptive quantum mechanical (QM) / molecular mechanical (MM) methods enable efficient molecular simulations of chemistry in solution by describing reactive subregions with an accurate many-body potential energy expression (QM) while the rest of the system is described in a more approximate manner (MM). As solvent molecules diffuse in and out of the reactive region, they are gradually included into (and excluded from) the many-body QM potential. It would be desirable to model such system 1 using an adaptive Hamiltonian, but so far it has resulted in distorted structures at the boundary between the two regions. Here, we propose a Hamiltonian scheme to describe adaptively solvent diffusion across a multi-scale boundary separating configurational potentials that cannot be expressed by a multi-body expansion. The adaptive expressions are entirely general, and complimentary to all standard (non-adaptive) QM/MM embedding schemes available. We demonstrate the validity of our approach on a system described by two different MM potentials (MM/MM'), in which long-range interactions are treated by many-body Ewald summation. Our Hamiltonian approach provides both energy conservation and the correct solvent structure everywhere in the system, thus enabling microcanonical adaptive QM/MM simulations that can be used to obtain vibrational spectra and dynamical properties.

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A two-dimensional energy surface for a type II SN2 reaction in aqueous solution

Cited by 125 publications

References 0 publications

Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates

Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates

A quantum mechanics-molecular mechanics study of dissociative electron transfer: The methylchloride radical anion in aqueous solution

Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials

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