Molecular dynamics simulations of ion solvation by flexible‐boundary QM/MM: On‐the‐fly partial charge transfer between QM and MM subsystems

Pezeshki, Soroosh; Lin, Hai

doi:10.1002/jcc.23685

Cited by 21 publications

(27 citation statements)

References 100 publications

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“…6(b), blue and red lines) demonstrate a strong affinity to build hydrogen bonds with water in agreement with QM/MM calculations. 145 The striking first peak of the corresponding Ow-distribution function is centered at 2.8 Å analogously to QM prediction for NH + 4 and CH 3 NH + 3 ions. 76 An average value for the water coordination number of Cl − is 6.79, which is close to experimental value of 6.…”

Section: Structural Analysis: Solvent Distribution Around Nanopartsupporting

confidence: 73%

Water around fullerene shape amphiphiles: A molecular dynamics simulation study of hydrophobic hydration

Varanasi

Guskova

John

et al. 2015

The Journal of Chemical Physics

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Fullerene C60 sub-colloidal particle with diameter ∼1 nm represents a boundary case between small and large hydrophobic solutes on the length scale of hydrophobic hydration. In the present paper, a molecular dynamics simulation is performed to investigate this complex phenomenon for bare C60 fullerene and its amphiphilic/charged derivatives, so called shape amphiphiles. Since most of the unique properties of water originate from the pattern of hydrogen bond network and its dynamics, spatial, and orientational aspects of water in solvation shells around the solute surface having hydrophilic and hydrophobic regions are analyzed. Dynamical properties such as translational-rotational mobility, reorientational correlation and occupation time correlation functions of water molecules, and diffusion coefficients are also calculated. Slower dynamics of solvent molecules—water retardation—in the vicinity of the solutes is observed. Both the topological properties of hydrogen bond pattern and the "dangling" -OH groups that represent surface defects in water network are monitored. The fraction of such defect structures is increased near the hydrophobic cap of fullerenes. Some "dry" regions of C60 are observed which can be considered as signatures of surface dewetting. In an effort to provide molecular level insight into the thermodynamics of hydration, the free energy of solvation is determined for a family of fullerene particles using thermodynamic integration technique.

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Section: Structural Analysis: Solvent Distribution Around Nanopartsupporting

confidence: 73%

Water around fullerene shape amphiphiles: A molecular dynamics simulation study of hydrophobic hydration

Varanasi

Guskova

John

et al. 2015

The Journal of Chemical Physics

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“…However, it has previously been shown that such a simple correction results in equilibrium solvent structures with an extreme depletion of solvent molecules across the T-region. 7,8,22 The depletion in the transition region can be explained using insights presented in the HAdResS paper. 17 The authors suggested that the energy release upon conversion of a particle…”

Section: 'Per Molecule' Correction To a Many-body Hamiltonianmentioning

confidence: 99%

“…Adaptive resolution methods address this issue by dynamically assigning molecules HR or LR character based on their proximity to the active site. [6][7][8][9][10][11][12][13] Generally, this procedure involves a transition region that connects smoothly the active and environment regions (T-region, Figure 1). The solvent molecules in the T-region have partial HR and partial LR character, and the description of each solvent molecule s smoothly changes from HR to LR (or vice versa) as it moves across the region.…”

Section: Introductionmentioning

confidence: 99%

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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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“…The electrostatic interaction between the QM and MM regions can be computed at the MM level of theory, and this is commonly referred to as mechanical embedding . A set of partial atomic charges must be generated for each atom in the QM region using a Mulliken (or similar) charge partitioning scheme.…”

Section: Embeddingmentioning

confidence: 99%

Adaptive quantum mechanics/molecular mechanics methods

Zheng

Waller

2016

WIREs Comput Mol Sci

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Multiscale methods have enjoyed a well-celebrated place in the computational chemists' toolbox, while the next generation of so-called adaptive quantum mechanics/molecular mechanics (QM/MM) methods were being developed on the fringe for the past 20 years. Adaptive QM/MM methods hold the promise of extending the range of applicability, currently at the expense of complexity and computational scaling. There are a number of challenges in the area; firstly, the ability to partition a system on the fly has led to the distance, number, density, and stress-based approaches. Secondly, methods that smoothen the transition from a QM to an MM region using a single configuration include Hot-Spot, ONIOM-XS, and time-adaptive. Alternatively, more computationally expensive methods that smoothen the transition region based on multiple configurations are the permuted and sorted adaptive permutation, difference-based adaptive, and size-consistent multipartitioning methods. There exist three alternative methods that avoid issues of smoothening altogether; they are the so-called buffered force, ABRUPT, and the flexible inner restraint methods. In this advanced review, an overview on the available methods, a number of applications, and the remaining challenges are discussed.

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Molecular dynamics simulations of ion solvation by flexible‐boundary QM/MM: On‐the‐fly partial charge transfer between QM and MM subsystems

Cited by 21 publications

References 100 publications

Water around fullerene shape amphiphiles: A molecular dynamics simulation study of hydrophobic hydration

Water around fullerene shape amphiphiles: A molecular dynamics simulation study of hydrophobic hydration

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

Adaptive quantum mechanics/molecular mechanics methods

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