Thermalized Drude Oscillators with the LAMMPS Molecular Dynamics Simulator

Dequidt, Alain; Devémy, Julien; Pádua, Agı́lio A. H.

doi:10.1021/acs.jcim.5b00612

Cited by 93 publications

(139 citation statements)

References 33 publications

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“…The degrees of freedom corresponding to the distances between the Drude particles and their cores were thermostated at 1 K 1 . Keeping the Drude degrees of freedom at low temperature generates a trajectory close to that of relaxed (self-consistent) Drudes, enabling trajectories with a timestep of 1 fs for the polarisable model, as was validated in the literature 1,6 .…”

Section: Methodsmentioning

confidence: 91%

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Resolving dispersion and induction components for polarisable molecular simulations of ionic liquids

Pádua

2017

The Journal of Chemical Physics

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One important development in interaction potential models, or atomistic force fields, for molecular simulation is the inclusion of explicit polarisation, which represents the induction effects of charged or polar molecules on polarisable electron clouds. Polarisation can be included through fluctuating charges, induced multipoles or Drude dipoles. This work uses Drude dipoles and is focused on room-temperature ionic liquids, for which fixed-charge models predict too slow dynamics. The aim of this study is to devise a strategy to adapt existing non-polarisable force fields upon addition of polarisation, because induction was already contained to an extent, implicitly, due to parametrisation against empirical data. Therefore, a fraction of the van der Waals interaction energy should be subtracted so that the Lennard-Jones terms only account for dispersion and the Drude dipoles for induction. Symmetry-adapted perturbation theory (SAPT) is used to resolve the dispersion and induction terms in dimers and to calculate scaling factors to reduce the Lennard-Jones terms from the non-polarisable model. Simply adding Drude dipoles to an existing fixed-charge model already improves the prediction of transport properties, increasing diffusion coefficients and lowering the viscosity. Scaling down the Lennard-Jones terms leads to still faster dynamics and to densities that match experiment extremely well. The concept developed here improves the overall prediction of density and transport properties and can be adapted to other models and systems. In terms of microscopic structure of the ionic liquids, the inclusion of polarisation and the down-scaling of Lennard-Jones terms affects onyl slightly the ordering of the first shell of counterions, leading to small decreases in coordination numbers. Remarkably, the effect of polarisation is major beyond first neighbours, significantly weakening spatial correlations, a structural effect that is certainly related to the faster dynamics of polarisable models.

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Section: Methodsmentioning

confidence: 91%

“…Drude polarisation was added to the non-polarisable systems using the polarizer tool, distributed with the LAMMPS package and described in detail in the literature 6 . The interested reader can thus generate files with the non-polarisable and polarisable force field parameters used in the present work.…”

Section: Methodsmentioning

confidence: 99%

Resolving dispersion and induction components for polarisable molecular simulations of ionic liquids

Pádua

2017

The Journal of Chemical Physics

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“…Since computational approaches based on the force field/ ab initio molecular dynamics (MD) simulation allow us to visualize the molecular structures of RTILs, they have been frequently used for connecting both the bulk [22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37] and interfacial structures [38][39][40][41][42][43][44] of RTILs with their physical and chemical properties. The non-polarizable force field MD (NP-FFMD) simulation was the first to be applied to RTILs.…”

Section: Introductionmentioning

confidence: 99%

“…[22][23][24][25] To improve the description of the dynamical properties of RTILs, polarizable force field MD has been applied for RTILs. 26,[33][34][35][36][37] The molecular polarizability of RTILs in the polarizable force field MD (P-FFMD) simulation screens the electrostatic interactions, accelerating the RTIL dynamics. 26 Furthermore, the interfacial structure of RTILs at the RTIL/air interface was examined using P-FFMD.…”

Section: Introductionmentioning

confidence: 99%

π⁺–π⁺ stacking of imidazolium cations enhances molecular layering of room temperature ionic liquids at their interfaces

Tang

Ohto

Hasegawa

et al. 2017

Phys. Chem. Chem. Phys.

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The interfacial structure of room temperature ionic liquids (RTILs) controls many of the unique properties of RTILs, such as the high capacitance of RTILs and the efficiency of charge transport between RTILs and electrodes. RTILs have been experimentally shown to exhibit interfacial molecular layering structures over a 10 Å length scale. However, the driving force behind the formation of these layered structures has not been resolved. Here, we report ab initio molecular dynamics simulations of imidazolium RTIL/air and RTIL/graphene interfaces along with force field molecular dynamics simulations. We find that the π-π interaction of imidazolium cations enhances the layering structure of RTILs, despite the electrostatic repulsion. The length scales of the molecular layering at the RTIL/air and RTIL/graphene interfaces are very similar, manifesting the limited effect of the substrate on the interfacial organization of RTILs.

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“…[65] Recently, a polarizable energy function based on thermal Drude oscillators was introduced in LAMMPS. [67,68] The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, acetone, and butanone) as shown in Figure 1 as well as their associated acyclic sugars (D-allose and D-psicose) as part of the development of a comprehensive polarizable force field for biomolecules.…”

Section: Introductionmentioning

confidence: 99%

Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates

Small

Aytenfisu

Lin

et al. 2017

J Comput Aided Mol Des

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The majority of computer simulations exploring biomolecular function employ Class I additive force fields (FF), which do not treat polarization explicitly. Accordingly, much effort has been made into developing models that go beyond the additive approximation. Development and optimization of the Drude polarizable FF has yielded parameters for selected lipids, proteins, DNA and a limited number of carbohydrates. The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, butaryaldehyde, isobutaryaldehyde, acetone, and butanone) as well as their associated acyclic sugars (D-allose and D-psicose). LJ parameters are optimized targeting experimental heats of vaporization and molecular volumes, while the electrostatic parameters are optimized targeting QM water interactions, dipole moments, and molecular polarizabilities. Bonded parameters are targeted to both QM and crystal survey values, with the models for ketones and aldehydes shown to be in good agreement with QM and experimental target data. The reported heats of vaporization and molecular volumes represent a compromise between the studied model compounds. Simulations of the model compounds show an increase in the magnitude and the fluctuations of the dipole moments in moving from gas phase to condensed phases, which is a phenomenon that the additive FF is intrinsically unable to reproduce. The result is a polarizable model for aliphatic ketones and aldehydes including the acyclic sugars D-allose and D-psicose, thereby extending the available biomolecules in the Drude polarizable FF.

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Thermalized Drude Oscillators with the LAMMPS Molecular Dynamics Simulator

Cited by 93 publications

References 33 publications

Resolving dispersion and induction components for polarisable molecular simulations of ionic liquids

Resolving dispersion and induction components for polarisable molecular simulations of ionic liquids

π⁺–π⁺ stacking of imidazolium cations enhances molecular layering of room temperature ionic liquids at their interfaces

Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates

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Thermalized Drude Oscillators with the LAMMPS Molecular Dynamics Simulator

Cited by 93 publications

References 33 publications

Resolving dispersion and induction components for polarisable molecular simulations of ionic liquids

Resolving dispersion and induction components for polarisable molecular simulations of ionic liquids

π+–π+ stacking of imidazolium cations enhances molecular layering of room temperature ionic liquids at their interfaces

Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates

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π⁺–π⁺ stacking of imidazolium cations enhances molecular layering of room temperature ionic liquids at their interfaces