Mesoscale Electrostatics Driving Particle Dynamics in Non-Homogeneous Dielectrics

<div>We introduce a density functional-based formalism to compute the electrostatic energy and forces for a mesoscopic system in the condensed phase, described with molecular resolution. The dielectric permittivity is variable in space, and it is dependent on the density fields of the individual particles present in the system. The electrostatic potential is obtained from standard numerical solutions of the generalized Poisson equation. The presence of a particle-dependent varying dielectrics produces the appearance of mesoscopic polarization forces, which are dependent on the local fluctuations of the permittivity, as well as of the electrostatic field. The proposed implementation is numerically robust, with an error on the Coulomb forces that can be systematically controlled by the mesh of spatial grid used for solving the generalized Poisson equation. We show that the method presented here is able to reproduce the concentration-dependent partitioning of an ideal salt in water/oil mixtures, in particular, reproducing the ∝ 1/epsilon dependency of the partition coefficient for the free ions predicted by Born theory. Moreover, this approach reproduces the correct electrostatic features of both dipolar and charged lipid bilayers, with positive membrane and dipole potentials. The sum of both Coulomb and polarization interactions inside the membrane yields a globally repulsive potential of mean force for the ions, independently on their charge. The computational efficiency of the method makes it particularly suitable for the description of large scale polyelectrolyte soft-matter systems.</div>

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A Practical Approach to Large Scale Electronic Structure Calculations in Electrolyte Solutions via Continuum-Embedded Linear-Scaling DFT

10.26434/chemrxiv.11743071 ◽

2020 ◽

Author(s):

Jacek Dziedzic ◽

Arihant Bhandari ◽

Lucian Anton ◽

Chao Peng ◽

James Womack ◽

...

Keyword(s):

Boundary Conditions ◽

Density Functional ◽

Large Scale ◽

Ethylene Carbonate ◽

Electrostatic Energy ◽

Open Boundary ◽

Linear Scaling ◽

Open Boundary Conditions ◽

Electrostatic Problem ◽

Poisson Boltzmann

We present the implementation of a hybrid continuum-atomistic model for including the effects of surrounding electrolyte in large-scale density functional theory (DFT) calculations within the ONETEP linear-scaling DFT code, which allows the simulation of large complex systems such as electrochemical interfaces. The model represents the electrolyte ions as a scalar field and the solvent as a polarisable dielectric continuum, both surrounding the quantum solute. The overall energy expression is a grand canonical functional incorporating the electron kinetic and exchange correlation energies, the total electrostatic energy, entropy and chemical potentials of surrounding electrolyte, osmotic pressure, and the effects of cavitation, dispersion and repulsion. The DFT calculation is performed fully self-consistently in the electrolyte model, allowing the quantum mechanical system and the surrounding continuum environment to interact and mutually polarize. A bespoke parallel Poisson-Boltzmann solver library, DL_MG, deals with the electrostatic problem, solving a generalized Poisson-Boltzmann equation. Our model supports open boundary conditions, which allows the treatment of molecules, entire biomolecules or larger nanoparticle assemblies in electrolyte. We have also implemented the model for periodic boundary conditions, allowing the treatment of extended systems such as electrode surfaces in contact with electrolyte. A key feature of the model is the use of solute-size and solvation-shell-aware accessibility functions that prevent the unphysical accumulation of electrolyte charge near the quantum solute boundary. The model has a small number of parameters: here we demonstrate their calibration against experimental mean activity coefficients. We also present an exemplar simulation of a 1634-atom model of the interface between a graphite anode and LiPF<sub>6</sub> electrolyte in ethylene carbonate solvent. We compare the cases where Li atoms are intercalated at opposite edges of the graphite slab and in solution, demonstrating a potential application of the model in simulations of fundamental processes in Li-ion batteries.

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A Practical Approach to Large Scale Electronic Structure Calculations in Electrolyte Solutions via Continuum-Embedded Linear-Scaling DFT

10.26434/chemrxiv.11743071.v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Jacek Dziedzic ◽

Arihant Bhandari ◽

Lucian Anton ◽

Chao Peng ◽

James Womack ◽

...

Keyword(s):

Boundary Conditions ◽

Density Functional ◽

Large Scale ◽

Ethylene Carbonate ◽

Electrostatic Energy ◽

Open Boundary ◽

Linear Scaling ◽

Open Boundary Conditions ◽

Electrostatic Problem ◽

Poisson Boltzmann

We present the implementation of a hybrid continuum-atomistic model for including the effects of surrounding electrolyte in large-scale density functional theory (DFT) calculations within the ONETEP linear-scaling DFT code, which allows the simulation of large complex systems such as electrochemical interfaces. The model represents the electrolyte ions as a scalar field and the solvent as a polarisable dielectric continuum, both surrounding the quantum solute. The overall energy expression is a grand canonical functional incorporating the electron kinetic and exchange correlation energies, the total electrostatic energy, entropy and chemical potentials of surrounding electrolyte, osmotic pressure, and the effects of cavitation, dispersion and repulsion. The DFT calculation is performed fully self-consistently in the electrolyte model, allowing the quantum mechanical system and the surrounding continuum environment to interact and mutually polarize. A bespoke parallel Poisson-Boltzmann solver library, DL_MG, deals with the electrostatic problem, solving a generalized Poisson-Boltzmann equation. Our model supports open boundary conditions, which allows the treatment of molecules, entire biomolecules or larger nanoparticle assemblies in electrolyte. We have also implemented the model for periodic boundary conditions, allowing the treatment of extended systems such as electrode surfaces in contact with electrolyte. A key feature of the model is the use of solute-size and solvation-shell-aware accessibility functions that prevent the unphysical accumulation of electrolyte charge near the quantum solute boundary. The model has a small number of parameters: here we demonstrate their calibration against experimental mean activity coefficients. We also present an exemplar simulation of a 1634-atom model of the interface between a graphite anode and LiPF<sub>6</sub> electrolyte in ethylene carbonate solvent. We compare the cases where Li atoms are intercalated at opposite edges of the graphite slab and in solution, demonstrating a potential application of the model in simulations of fundamental processes in Li-ion batteries.

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Multi-Scale Modelling of Aggregation of TiO2 Nanoparticle Suspensions in Water

Nanomaterials ◽

10.3390/nano12020217 ◽

2022 ◽

Vol 12 (2) ◽

pp. 217

Author(s):

Giulia Mancardi ◽

Matteo Alberghini ◽

Neus Aguilera-Porta ◽

Monica Calatayud ◽

Pietro Asinari ◽

...

Keyword(s):

Titanium Dioxide ◽

Density Functional ◽

Large Scale ◽

Molecular Descriptors ◽

Titanium Dioxide Nanoparticles ◽

Accurate Determination ◽

Potential Of Mean Force ◽

Multi Scale ◽

Spherical Bead ◽

Dynamics Simulations

Titanium dioxide nanoparticles have risen concerns about their possible toxicity and the European Food Safety Authority recently banned the use of TiO2 nano-additive in food products. Following the intent of relating nanomaterials atomic structure with their toxicity without having to conduct large-scale experiments on living organisms, we investigate the aggregation of titanium dioxide nanoparticles using a multi-scale technique: starting from ab initio Density Functional Theory to get an accurate determination of the energetics and electronic structure, we switch to classical Molecular Dynamics simulations to calculate the Potential of Mean Force for the connection of two identical nanoparticles in water; the fitting of the latter by a set of mathematical equations is the key for the upscale. Lastly, we perform Brownian Dynamics simulations where each nanoparticle is a spherical bead. This coarsening strategy allows studying the aggregation of a few thousand nanoparticles. Applying this novel procedure, we find three new molecular descriptors, namely, the aggregation free energy and two numerical parameters used to correct the observed deviation from the aggregation kinetics described by the Smoluchowski theory. Ultimately, molecular descriptors can be fed into QSAR models to predict the toxicity of a material knowing its physicochemical properties, enabling safe design strategies.

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Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport

Beilstein Journal of Nanotechnology ◽

10.3762/bjnano.4.65 ◽

2013 ◽

Vol 4 ◽

pp. 567-587 ◽

Cited By ~ 40

Author(s):

Pavel V Komarov ◽

Pavel G Khalatur ◽

Alexei R Khokhlov

Keyword(s):

Molecular Dynamics ◽

Density Functional ◽

Large Scale ◽

Water Channel ◽

Ion Association ◽

Characteristic Size ◽

Potential Of Mean Force ◽

Nafion Membrane ◽

Quantum Molecular Dynamics ◽

Ion Conducting

Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic) and minority (hydrophilic) subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25–50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping) mechanism as a significant contributor to the proton conductivity.

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Numerical solutions to the Poisson equation in media surrounding multiple arbitrarily shaped bodies

10.32469/10355/12185 ◽

2010 ◽

Author(s):

Zebadiah M. Smith

Keyword(s):

Poisson Equation ◽

Numerical Solutions ◽

The Poisson Equation

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Benchmark of Simplified Time-Dependent Density Functional Theory for UV-Vis Spectral Properties of Porphyrinoids

10.26434/chemrxiv.9912860 ◽

2019 ◽

Author(s):

Kamal Batra ◽

Stefan Zahn ◽

Thomas Heine

Keyword(s):

Density Functional Theory ◽

Density Functional ◽

Large Scale ◽

Absolute Error ◽

Time Dependent ◽

Basis Set ◽

Basis Sets ◽

Functional Theory ◽

Framework Materials ◽

Dependent Density

<p>We thoroughly benchmark time-dependent density- functional theory for the predictive calculation of UV/Vis spectra of porphyrin derivatives. With the aim to provide an approach that is computationally feasible for large-scale applications such as biological systems or molecular framework materials, albeit performing with high accuracy for the Q-bands, we compare the results given by various computational protocols, including basis sets, density-functionals (including gradient corrected local functionals, hybrids, double hybrids and range-separated functionals), and various variants of time-dependent density-functional theory, including the simplified Tamm-Dancoff approximation. An excellent choice for these calculations is the range-separated functional CAM-B3LYP in combination with the simplified Tamm-Dancoff approximation and a basis set of double-ζ quality def2-SVP (mean absolute error [MAE] of ~0.05 eV). This is not surpassed by more expensive approaches, not even by double hybrid functionals, and solely systematic excitation energy scaling slightly improves the results (MAE ~0.04 eV). </p>

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Sensitivity of Intra- and Intermolecular Interactions of Benzo[h]quinoline from Car–Parrinello Molecular Dynamics and Electronic Structure Inspection

International Journal of Molecular Sciences ◽

10.3390/ijms22105220 ◽

2021 ◽

Vol 22 (10) ◽

pp. 5220

Author(s):

Jarosław J. Panek ◽

Joanna Zasada ◽

Bartłomiej M. Szyja ◽

Beata Kizior ◽

Aneta Jezierska

Keyword(s):

Molecular Dynamics ◽

Electronic Structure ◽

Hydrogen Bonds ◽

Density Functional ◽

Quantum Effects ◽

Potential Of Mean Force ◽

Probability Density Distribution ◽

Donor And Acceptor ◽

Nuclear Quantum Effects ◽

Vibrational Features

The O-H...N and O-H...O hydrogen bonds were investigated in 10-hydroxybenzo[h]quinoline (HBQ) and benzo[h]quinoline-2-methylresorcinol complex in vacuo, solvent and crystalline phases. The chosen systems contain analogous donor and acceptor moieties but differently coupled (intra- versus intermolecularly). Car–Parrinello molecular dynamics (CPMD) was employed to shed light onto principle components of interactions responsible for the self-assembly. It was applied to study the dynamics of the hydrogen bonds and vibrational features as well as to provide initial geometries for incorporation of quantum effects and electronic structure studies. The vibrational features were revealed using Fourier transformation of the autocorrelation function of atomic velocity and by inclusion of nuclear quantum effects on the O-H stretching solving vibrational Schrödinger equation a posteriori. The potential of mean force (Pmf) was computed for the whole trajectory to derive the probability density distribution and for the O-H stretching mode from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling and nuclear quantum effects. The electronic structure changes of the benzo[h]quinoline-2-methylresorcinol dimer and trimers were studied based on Constrained Density Functional Theory (CDFT) whereas the Electron Localization Function (ELF) method was applied for all systems. It was found that the bridged proton is localized on the donor side in both investigated systems in vacuo. The crystalline phase simulations indicated bridged proton-sharing and transfer events in HBQ. These effects are even more pronounced when nuclear quantization is taken into account, and the quantized Pmf allows the proton to sample the acceptor area more efficiently. The CDFT indicated the charge depletion at the bridged proton for the analyzed dimer and trimers in solvent. The ELF analysis showed the presence of the isolated proton (a signature of the strongest hydrogen bonds) only in some parts of the HBQ crystal simulation. The collected data underline the importance of the intramolecular coupling between the donor and acceptor moieties.

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Tensor-structured algorithm for reduced-order scaling large-scale Kohn–Sham density functional theory calculations

npj Computational Materials ◽

10.1038/s41524-021-00517-5 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Chih-Chuen Lin ◽

Phani Motamarri ◽

Vikram Gavini

Keyword(s):

Density Functional Theory ◽

Density Functional ◽

Large Scale ◽

Density Functional Theory Calculations ◽

System Size ◽

Real Space ◽

Functional Theory ◽

Reduced Order ◽

Separable Approximation ◽

Tensor Basis

AbstractWe present a tensor-structured algorithm for efficient large-scale density functional theory (DFT) calculations by constructing a Tucker tensor basis that is adapted to the Kohn–Sham Hamiltonian and localized in real-space. The proposed approach uses an additive separable approximation to the Kohn–Sham Hamiltonian and an L1 localization technique to generate the 1-D localized functions that constitute the Tucker tensor basis. Numerical results show that the resulting Tucker tensor basis exhibits exponential convergence in the ground-state energy with increasing Tucker rank. Further, the proposed tensor-structured algorithm demonstrated sub-quadratic scaling with system-size for both systems with and without a gap, and involving many thousands of atoms. This reduced-order scaling has also resulted in the proposed approach outperforming plane-wave DFT implementation for systems beyond 2000 electrons.

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Bayesian active learning of interatomic force field for molecular dynamics simulation of Pt/Ag(111)

10.26434/chemrxiv-2021-sk6lf-v2 ◽

2021 ◽

Author(s):

Kai Xu ◽

Lei Yan ◽

Bingran You

Keyword(s):

Molecular Dynamics ◽

Active Learning ◽

Force Field ◽

Density Functional ◽

Process Model ◽

Large Scale ◽

Computational Cost ◽

Dynamics Simulation ◽

Potential Energy Landscape ◽

Three Body

Force field is a central requirement in molecular dynamics (MD) simulation for accurate description of the potential energy landscape and the time evolution of individual atomic motions. Most energy models are limited by a fundamental tradeoff between accuracy and speed. Although ab initio MD based on density functional theory (DFT) has high accuracy, its high computational cost prevents its use for large-scale and long-timescale simulations. Here, we use Bayesian active learning to construct a Gaussian process model of interatomic forces to describe Pt deposited on Ag(111). An accurate model is obtained within one day of wall time after selecting only 126 atomic environments based on two- and three-body interactions, providing mean absolute errors of 52 and 142 meV/Å for Ag and Pt, respectively. Our work highlights automated and minimalistic training of machine-learning force fields with high fidelity to DFT, which would enable large-scale and long-timescale simulations of alloy surfaces at first-principles accuracy.

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