Flexible simple point-charge water model with improved liquid-state properties

Wu, Yujie; Tepper, H.L.; Voth, Gregory A.

doi:10.1063/1.2136877

Cited by 1,095 publications

(1,164 citation statements)

References 70 publications

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“…25,26 The first sharp peak is located at 2.8Å from the central oxygen atom, and the second and third much shallower peaks lie at 4.4Å and 6.7Å respectively (Figure 4, red line). We use this result as a reference for the performance of the Hamiltonian simulations.…”

Section: Resultsmentioning

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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Section: Resultsmentioning

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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“…42 It was also shown to be superior to other water models 43,44 and has been recommended for modeling aqueous solutions of biomolecules. 45 It has also been previously employed in systems comprising interactions similar to those of the present work.…”

Section: Methodsmentioning

confidence: 99%

Solubilization of Poly{1,4-phenylene-[9,9-bis(4-phenoxy-butylsulfonate)]fluorene-2,7-diyl} in Water by Nonionic Amphiphiles

et al. 2009

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In the presence of the nonionic alkyloxyethylene surfactant n-dodecylpentaoxyethylene glycol ether (C 12 E 5 ), the anionic conjugated polyelectrolyte (CPE) poly{1,4-phenylene-[9,9-bis(4-phenoxy-butylsulfonate)]fluorene-2,7-diyl} (PBS-PFP) dissolves in water, leading to a blue shift in fluorescence and dramatic increases in fluorescence quantum yields above the surfactant critical micelle concentration (cmc). No significant changes were seen with a poly(ethylene oxide) of similar size to the surfactant headgroup, confirming that specific surfactant-polyelectrolyte interactions are important. From UV-visible and fluorescence spectroscopy, dynamic light scattering (DLS), small-angle X-ray scattering (SAXS), cryogenic transmission electron microscopy (cryo-TEM), and electrical conductivity, together with our published NMR and small-angle neutron scattering (SANS) results, we provide a coherent model for this behavior in terms of breakup of PBS-PFP clusters through polymer-surfactant association leading to cylindrical aggregates containing isolated polymer chains. This is supported by molecular dynamics simulations, which indicate stable polymer-surfactant structures and also provide indications of the tendency of C 12 E 5 to break up polymer clusters to form these mixed polymer-surfactant aggregates. Radial electron density profiles of the cylindrical cross section obtained from SAXS results reveal the internal structure of such inhomogeneous species. DLS and cryo-TEM results show that at higher surfactant concentrations the micelles start to grow, possibly partially due to formation of long, threadlike species. Other alkyloxyethylene surfactants, together with poly(propylene glycol) and hydrophobically modified poly(ethylene glycol), also solubilize this polymer in water, and it is suggested that this results from a balance between electrostatic (or ion-dipole), hydrophilic, and hydrophobic interactions. There is a small, but significant, dependence of the emission maximum on the local environment.

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“…On the other hand, the classical-mechanics water dimer interaction, of nearly 7.4 kcal/mol, is clearly above the available experimental data. The reason for this overestimation is that the SPC and SPC/Fw potentials, as most water force-fields, are parameterized to reflect the properties of the bulk liquid phase [29,43], where the molecular dipole moments are significantly enhanced with respect to the isolated molecule (see next section). As a matter of fact, the minimum of the MM curve, at nearly 2.7Å, is coincident with the first peak of the oxygen-oxygen radial distribution function (RDF) for liquid water at room temperature.…”

Section: Assessment Of the Model: Water Dimer And Aqueous Liquid Phasementioning

confidence: 99%

“…The MM subsystem in the present study involved H 2 O molecules, which were described through the SPC flexible water model (SPC/Fw) proposed by Wu, Tepper and Voth [29]. The same set of parameters for σ and were used in both the MM-MM and the QM-MM non-electrostatic interactions, given respectively in equations 6 and 18.…”

Section: Total Energy In the Qm-mm Implementationmentioning

confidence: 99%

A quantum-mechanics molecular-mechanics scheme for extended systems

Hunt¹,

Sánchez²,

Scherlis³

2016

J. Phys.: Condens. Matter

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We introduce and discuss a hybrid quantum-mechanics molecular-mechanics (QM-MM) approach for Car-Parrinello DFT simulations with pseudopotentials and planewaves basis, designed for the treatment of periodic systems. In this implementation the MM atoms are considered as additional QM ions having fractional charges of either sign, which provides conceptual and computational simplicity by exploiting the machinery already existing in planewave codes to deal with electrostatics in periodic boundary conditions.With this strategy, both the QM and MM regions are contained in the same supercell, which determines the periodicity for the whole system. Thus, while this method is not meant to compete with non-periodic QM-MM schemes able to handle extremely large but finite MM regions, it is shown that for periodic systems of a few hundred atoms, our approach provides substantial savings in computational times by treating classically a fraction of the particles. The performance and accuracy of the method is assessed through the study of energetic, structural, and dynamical aspects of the water dimer and of the aqueous bulk phase. Finally, the QM-MM scheme is applied to the computation of the vibrational spectra of water layers adsorbed at the TiO 2 anatase (101) solid-liquid interface. This investigation suggests that the inclusion of a second monolayer of H 2 O molecules is sufficient to induce on the first adsorbed layer, a vibrational dynamics similar to that taking place in the presence of an aqueous environment. The present QM-MM scheme appears as a very interesting tool to efficiently perform molecular dynamics simulations of complex condensed matter systems, from solutions to nanoconfined fluids to different kind of interfaces.

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Flexible simple point-charge water model with improved liquid-state properties

Cited by 1,095 publications

References 70 publications

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

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

Solubilization of Poly{1,4-phenylene-[9,9-bis(4-phenoxy-butylsulfonate)]fluorene-2,7-diyl} in Water by Nonionic Amphiphiles

A quantum-mechanics molecular-mechanics scheme for extended systems

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