Quantum mechanical study of solvent effects in a prototype S<i>N</i>2 reaction in solution: Cl− attack on CH3Cl

Kuechler, Erich R.; York, Darrin M.

doi:10.1063/1.4863344

Cited by 18 publications

(35 citation statements)

References 69 publications

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“…For all QM/MM calculations reported here, we employ the recently developed Specific Reaction Parameterization (SRP) AM1 Hamiltonian for Cl − attack on CH 3 Cl that has been demonstrated to accurately model this reaction in both the gas phase and in solution. 40 All non-QXD atoms in QM/MM simulations and calculations performed will use the LJ parameters provided in Table I.…”

Section: B Specific Reaction Parameterization Hamiltonianmentioning

confidence: 99%

“…Free energy profile simulations were performed in order to test the effects of the QXD model on the attack barrier of a chloride anion reacting with methylchloride. In previous studies, 40 the traditional LJ model was shown to accurately capture this reaction barrier while using the LJ Cl − parameters set. The QXD parameter set used for these simulations is the set used to recapitulate experimental solvation free energies outlined in Subsection IV C. Results of these simulations, and comparisons to the standard LJ model with both the LJ Cl − and LJ CH 3 Cl parameter sets, can be seen in Figure 4.…”

Section: Qxd and Lj Free Energy Profilesmentioning

confidence: 99%

“…In the present work, we examine a well-studied benchmark reaction of the chloride ion attack on methylchloride using a specific reaction parameterization semiempirical QM model 40 in a solution of non-polarizable MM water while treating electrostatic QM/MM interactions via electrostatic embedding. This combination of QM and MM models is widely used in combined QM/MM studies of biological reactions, a target application area for which the hope is that the methods introduced here will have future impact.…”

Section: Introductionmentioning

confidence: 99%

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Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

Kuechler

Giese

York

2015

The Journal of Chemical Physics

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Accurate modeling of the molecular environment is critical in condensed phase simulations of chemical reactions. Conventional quantum mechanical/molecular mechanical (QM/MM) simulations traditionally model non-electrostatic non-bonded interactions through an empirical Lennard-Jones (LJ) potential which, in violation of intuitive chemical principles, is bereft of any explicit coupling to an atom's local electronic structure. This oversight results in a model whereby short-ranged exchange-repulsion and long-ranged dispersion interactions are invariant to changes in the local atomic charge, leading to accuracy limitations for chemical reactions where significant atomic charge transfer can occur along the reaction coordinate. The present work presents a variational, charge-dependent exchange-repulsion and dispersion model, referred to as the charge-dependent exchange and dispersion (QXD) model, for hybrid QM/MM simulations. Analytic expressions for the energy and gradients are provided, as well as a description of the integration of the model into existing QM/MM frameworks, allowing QXD to replace traditional LJ interactions in simulations of reactive condensed phase systems. After initial validation against QM data, the method is demonstrated by capturing the solvation free energies of a series of small, chlorine-containing compounds that have varying charge on the chlorine atom. The model is further tested on the SN2 attack of a chloride anion on methylchloride. Results suggest that the QXD model, unlike the traditional LJ model, is able to simultaneously obtain accurate solvation free energies for a range of compounds while at the same time closely reproducing the experimental reaction free energy barrier. The QXD interaction model allows explicit coupling of atomic charge with many-body exchange and dispersion interactions that are related to atomic size and provides a more accurate and robust representation of non-electrostatic non-bonded QM/MM interactions.

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Section: B Specific Reaction Parameterization Hamiltonianmentioning

confidence: 99%

Section: Qxd and Lj Free Energy Profilesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

Kuechler

Giese

York

2015

The Journal of Chemical Physics

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“…With this in mind, we wanted to understand how well NDDO methods perform for the description of bulk water. As a first test, we focus on a popular NDDO method, PM6, and look at an important structural descriptor of water, the oxygen–oxygen pair distribution function (Fig. ).…”

Section: Introductionmentioning

confidence: 99%

Why many semiempirical molecular orbital theories fail for liquid water and how to fix them

2015

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Water is an extremely important liquid for chemistry and the search for more accurate force fields for liquid water continues unabated. Neglect of diatomic differential overlap (NDDO) molecular orbital methods provide and intriguing generalization of classical force fields in this regard because they can account both for bond breaking and electronic polarization of molecules. However, we show that most standard NDDO methods fail for water because they give an incorrect description of hydrogen bonding, water's key structural feature. Using force matching, we design a reparameterized NDDO model and find that it qualitatively reproduces the experimental radial distribution function of water, as well as various monomer, dimer, and bulk properties that PM6 does not. This suggests that the apparent limitations of NDDO models are primarily due to poor parameterization and not to the NDDO approximations themselves. Finally, we identify the physical parameters that most influence the condensed phase properties. These results help to elucidate the chemistry that a semiempirical molecular orbital picture of water must capture. We conclude that properly parameterized NDDO models could be useful for simulations that require electronically detailed explicit solvent, including the calculation of redox potentials and simulation of charge transfer and photochemistry.

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“…4,6,[15][16][17][18][19][20][21][22] These phenomena are especially apparent when studying highly charged systems such as RNA 11 as shown in Figure 1. To model these effects, simulations can be performed that include a vast buffer of explicit solvent molecules; however, such approaches are often extremely computationally demanding.…”

Section: Introductionmentioning

confidence: 99%

VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions

Kuechler

Giese

York

2016

The Journal of Chemical Physics

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To better represent the solvation effects observed along reaction pathways, and of ionic species in general, a charge-dependent variable-radii smooth conductor-like screening model (VR-SCOSMO) is developed. This model is implemented and parameterized with a third order density-functional tight binding quantum model, DFTB3/3OB-OPhyd, a quantum method which was developed for organic and biological compounds, utilizing a specific parameterization for phosphate hydrolysis reactions. Unlike most other applications with the DFTB3/3OB model, an auxiliary set of atomic multipoles is constructed from the underlying DFTB3 density matrix which is used to interact the solute with the solvent response surface. The resulting method is variational, produces smooth energies, and has analytic gradients. As a baseline, a conventional SCOSMO model with fixed radii is also parameterized. The SCOSMO and VR-SCOSMO models shown have comparable accuracy in reproducing neutral-molecule absolute solvation free energies; however, the VR-SCOSMO model is shown to reduce the mean unsigned errors (MUEs) of ionic compounds by half (about 2-3 kcal/mol).

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Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl− attack on CH3Cl

Cited by 18 publications

References 69 publications

Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

Why many semiempirical molecular orbital theories fail for liquid water and how to fix them

VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions

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