Polarizable Model Research Articles

First‐Principles Study on the Crystalline Ga4Sb6Te3 Phase Change Compound

The compound on the pseudobinary tie‐line is proposed in the literature as a phase change material with high crystallization temperature. Herein, the crystal structure of this compound is uncovered by means of a genetic algorithm and electronic structure calculations based on density functional theory. As opposed to the parent GaSb compound which crystallizes in the zincblende structure, the compound features an octahedral‐like coordination for Ga as well as for Sb and Te atoms. Other structures close in energy to the ground state are also proposed, including some with a tetrahedral‐like coordination of Ga atoms. Raman spectra computed within density functional perturbation theory and an empirical Bond Polarizability Model are shown to be able to discriminate among the different possible local environments of Ga atoms.

Diffusion of ions and solvent in propylene carbonate solutions for lithium-ion battery applications

Diffusion of lithium ions in organic solvent solutions is important to the performance of lithium ion batteries. In this article, fully atomistic molecular dynamics (MD) simulations were employed to study the diffusive behavior of LiPF6 electrolyte salt and propylene carbonate in solutions at different temperatures in direct comparison to experimental diffusivity data. Organic solutions at 1 M concentrations were considered at the operational conditions of Lithium ion batteries. We show that non-polarizable scaled charge force fields can predict, quantitatively, the diffusion of Li+ and PC solvent in a range of operational temperatures. Such type of force fields are much less computational demanding than polarizable or ReaxFF models. Diffusion follows an Arrhenius type of behavior. van Hove autocorrelation functions show a nonGaussian type of movement for ions and PC solvent. The Li+ is moving by a mixed-vehicular mechanism. Moreover, the nearest neighbour distances of the Li+- carbonyl oxygen in these PC solutions is predicted accurately using the scaled charges GAFF, in agreement to experiments. Furthermore, quantitative prediction of modeled ionic conductivity in comparison to experiments can be achieved in a range of temperatures.

Efficient formulation of polarizable Gaussian multipole electrostatics for biomolecular simulations.

Molecular dynamics simulations of biomolecules have been widely adopted in biomedical studies. As classical point-charge models continue to be used in routine biomolecular applications, there have been growing demands on developing polarizable force fields for handling more complicated biomolecular processes. Here, we focus on a recently proposed polarizable Gaussian Multipole (pGM) model for biomolecular simulations. A key benefit of pGM is its screening of all short-range electrostatic interactions in a physically consistent manner, which is critical for stable charge-fitting and is needed to reproduce molecular anisotropy. Another advantage of pGM is that each atom's multipoles are represented by a single Gaussian function or its derivatives, allowing for more efficient electrostatics than other Gaussian-based models. In this study, we present an efficient formulation for the pGM model defined with respect to a local frame formed with a set of covalent basis vectors. The covalent basis vectors are chosen to be along each atom's covalent bonding directions. The new local frame can better accommodate the fact that permanent dipoles are primarily aligned along covalent bonds due to the differences in electronegativity of bonded atoms. It also allows molecular flexibility during molecular simulations and facilitates an efficient formulation of analytical electrostatic forces without explicit torque computation. Subsequent numerical tests show that analytical atomic forces agree excellently with numerical finite-difference forces for the tested system. Finally, the new pGM electrostatics algorithm is interfaced with the particle mesh Ewald (PME) implementation in Amber for molecular simulations under the periodic boundary conditions. To validate the overall pGM/PME electrostatics, we conducted an NVE simulation for a small water box of 512 water molecules. Our results show that to achieve energy conservation in the polarizable model, it is important to ensure enough accuracy on both PME and induction iteration. It is hoped that the reformulated pGM model will facilitate the development of future force fields based on the pGM electrostatics for applications in biomolecular systems and processes where polarization plays crucial roles.

Transferable interactions of Li+ and Mg2+ ions in polarizable models.

Therapeutic implications of Li+, in many cases, stem from its ability to inhibit certain Mg2+-dependent enzymes, where it interacts with or substitutes for Mg2+. The underlying details of its action are, however, unknown. Molecular simulations can provide insights, but their reliability depends on how well they describe relative interactions of Li+ and Mg2+ with water and other biochemical groups. Here, we explore, benchmark, and recommend improvements to two simulation approaches: the one that employs an all-atom polarizable molecular mechanics (MM) model and the other that uses a hybrid quantum and MM implementation of the quasi-chemical theory (QCT). The strength of the former is that it describes thermal motions explicitly and that of the latter is that it derives local contributions from electron densities. Reference data are taken from the experiment, and also obtained systematically from CCSD(T) theory, followed by a benchmarked vdW-inclusive density functional theory. We find that the QCT model predicts relative hydration energies and structures in agreement with the experiment and without the need for additional parameterization. This implies that accurate descriptions of local interactions are essential. Consistent with this observation, recalibration of local interactions in the MM model, which reduces errors from 10.0 kcal/mol to 1.4 kcal/mol, also fixes aqueous phase properties. Finally, we show that ion-ligand transferability errors in the MM model can be reduced significantly from 10.3 kcal/mol to 1.2 kcal/mol by correcting the ligand's polarization term and by introducing Lennard-Jones cross-terms. In general, this work sets up systematic approaches to evaluate and improve molecular models of ions binding to proteins.

What is the Optimal Size of the Quantum Region in Embedding Calculations of Two-Photon Absorption Spectra of Fluorescent Proteins?

We systematically investigate an impact of the size and content of a quantum (QM) region, treated at the density functional theory level, in embedding calculations on one- (OPA) and two-photon absorption (TPA) spectra of the following fluorescent proteins (FPs) models: Aequorea victoria green FP (avGFP) with neutral (avGFP-n) and anionic (avGFP-a) chromophore as well as Citrine FP. We find that amino acid (a.a.) residues as well as water molecules hydrogen-bonded (h-bonded) to the chromophore usually boost both OPA and TPA processes intensity. The presence of hydrophobic a.a. residues in the quantum region also non-negligibly affects both absorption spectra but decreases absorption intensity. We conclude that to reach a quantitative description of OPA and TPA spectra in multiscale modeling of FPs, the quantum region should consist of a chromophore and most of a.a. residues and water molecules in a radius of 0.30–0.35 nm (ca. 200–230 atoms) when the remaining part of the system is approximated by the electrostatic point-charges. The optimal size of the QM region can be reduced to 80–100 atoms by utilizing a more advanced polarizable embedding model. We also find components of the QM region that are specific to a FP under study. We propose that the F165 a.a. residue is important in tuning the TPA spectrum of avGFP-n but not other investigated FPs. In the case of Citrine, Y203 and M69 a.a. residues must definitely be part of the QM subsystem. Furthermore, we find that long-range electrostatic interactions between the QM region and the rest of the protein cannot be neglected even for the most extensive QM regions (ca. 350 atoms).

Encapsulation effect of π-conjugated quaterthiophene on the radial breathing and tangential modes of semiconducting and metallic single-walled carbon nanotubes.

We developed a hybrid approach, combining the density functional theory, molecular mechanics, bond polarizability model and the spectral moment's method to compute the nonresonant Raman spectra of a single quaterthiophene (4T) molecule encapsulated into a single-walled carbon nanotube (metallic or semiconducting). We reported the optimal tube diameter allowing the 4T encapsulation. The influence of the encapsulation on the Raman modes of the 4T molecule and those of the nanotube (radial breathing modes and tangential modes) are analyzed. An eventual charge transfer between the 4T oligomer and the nanotube is discussed.

SEM-Drude Model for the Accurate and Efficient Simulation of MgCl2-KCl Mixtures in the Condensed Phase.

There is a long history of models that to different extents reproduce structural and dynamical properties of high-temperature molten salts. Whereas rigid ion models can work fairly well for some of the monovalent salts, polarizability is fundamentally important when small divalent or multivalent cations are combined with significantly polarizable anions such as Cl- to form networked liquids that display a first sharp diffraction peak. There are excellent polarizable ion models (PIMs) for these systems, but there has been little success with the less expensive Core-Shell type models, which are often described as unwieldy or difficult to fit. In this article, we present the Sharma-Emerson-Margulis (SEM)-Drude model for MgCl2/KCl mixtures that with the same ingredients used in the latest and most accurate PIM models overcome the aforementioned obstacles at significantly less computational cost; structural and dynamical properties are for all practical purposes very similar to what we obtain from the PIM but typical simulations can be more than 30 times faster. This has allowed us not only to expand our recent studies on the temperature and composition dependence of intermediate range order in MgCl2/KCl mixtures but also to access transport properties that were simply too costly to properly sample in our recently published studies.

How good are polarizable and flexible models for water: Insights from a many-body perspective.

We present a systematic analysis of state-of-the-art polarizable and flexible water models from a many-body perspective, with a specific focus on their ability to represent the Born-Oppenheimer potential energy surface of water from the gas to the liquid phase. Using coupled cluster data in the completed basis set limit as a reference, we examine the accuracy of the polarizable models in reproducing individual many-body contributions to interaction energies and harmonic frequencies of water clusters and compare their performance with that of MB-pol, an explicit many-body model that has been shown to correctly predict the properties of water across the entire phase diagram. Based on these comparisons, we use MB-pol as a reference to analyze the ability of the polarizable models to reproduce the energy landscape of liquid water under ambient conditions. We find that, while correctly reproducing the energetics of minimum-energy structures, the polarizable models examined in this study suffer from inadequate representations of many-body effects for distorted configurations. To investigate the role played by geometry-dependent representations of 1-body charge distributions in reproducing coupled cluster data for both interaction and many-body energies, we introduce a simplified version of MB-pol that adopts fixed atomic charges and demonstrate that the new model retains the same accuracy as the original MB-pol model. Based on the analyses presented in this study, we believe that future developments of both polarizable and explicit many-body models should continue in parallel and would benefit from synergistic efforts aimed at integrating the best aspects of the two theoretical/computational frameworks.

Two-Dimensional Infrared Spectroscopy of Aqueous Solutions of Metal Nitrates: Slowdown of Spectral Diffusion in the Presence of Divalent Cations.

The hydrogen-bonded network of water can be affected both structurally and dynamically by the presence of ions. In the present study, we have considered three aqueous solutions of metal nitrates to investigate the effects of divalent cations (Mg2+ and Ca2+), compared to that of monovalent Na+ ions, on hydrogen-bond fluctuations and vibrational spectral diffusion through calculations of linear and two-dimensional infrared spectra of these solutions at room temperature. We have employed the methods of molecular dynamics simulations using effective polarizable models of ions combined with quantum mechanical calculations of transition variables and statistical mechanical calculations of spectral response functions of vibrational spectroscopy. Divalent cations are found to have much stronger and longer-ranged effects on the structure and dynamics of the hydrogen-bonded network than that induced by the monovalent sodium ions. The blue shifts in the calculated linear spectra are found to follow the Hofmeister trend for the cations. The 2D-IR spectral lineshape and intensity corresponding to three-pulse echo peak shift (3PEPS) experiments are calculated. The timescales of these nonlinear spectral responses and also frequency-time correlations show significant slowing down of spectral diffusion for solutions containing divalent Mg2+ and Ca2+ ions compared to the corresponding dynamics of the solution containing Na+ ions. Unlike NaNO3 solution, the relaxation of frequency and dipole orientational fluctuations of anion-bound water in Mg(NO3)2 and Ca(NO3)2 solutions are found to be somewhat slower than bulk water, which can be attributed to the presence of divalent cations whose effects go beyond their first solvation shells. This is also seen in the dynamics of bulk water in these solutions which is found to be notably slower for the solutions containing divalent cations than that in the NaNO3 solution. Unlike Mg2+ and Ca2+ ions, no specific cationic effect is observed for the Na+ ions.

A Transferable Polarizable Force Field for Urea Crystals and Aqueous Solutions.

Urea is an important chemical with many biological and industrial applications. In this work, we develop a first-principles polarizable force field for urea crystals and aqueous solutions within the symmetry-adapted perturbation theory (SAPT) protocol with the SWM4-NDP model for water. We make three adjustments to the SAPT force field protocol: We augment the carbonyl oxygen atom of urea with additional interaction sites in order to address the "chelated" bent double hydrogen bonds in urea, we reduce the polarizability of urea by a factor of 0.70 to reproduce experimental in-crystal dipole moments, and we re-fit atomic pre-exponential parameters to correct the predicted liquid structure. We find that the resulting force field is in good agreement for the static and dynamic properties of aqueous urea solutions when compared to experiment or first-principles molecular dynamics simulations. The polarizable urea model accurately reproduces the crystal-solution phase diagram in the temperature range of 261 to 310 K; for which, it is superior to non-polarizable models. We expect that this force field will be useful in the modeling of complex biomolecular systems and enable studies of polarizability effects of solid-liquid phase behavior of complex fluids.

Vibrational Probe of Aqueous Electrolytes: The Field Is Not Enough

In this work, we study the vibrational solvatochromism and dynamics of dilute acetone as a carbonyl probe in simple aqueous electrolytes as a function of salt composition and concentration. We observe a linear dependence of the redshift of the CO stretch mode as a function of concentration for each salt, with the magnitude of the effect scaling with the charge densities of the cations. Using molecular dynamics (MD) simulations, we compare the observed spectral shifts with the electrostatic field distributions imparted on the acetone O, comparing a fixed-charge model and a polarizable model, and find that the experimentally observed frequencies scale linearly with the electric field for a given salt, but there remains a substantial component of the solvatochromism that depends on the identity of the cation and apparently cannot be explained by the electrostatic fields alone. Finally, we use ultrafast 2D IR spectroscopy to study the salt dependence of the solvation dynamics. We observe an anomalous nonmonotonic dependence of the time scale of the dynamics on the salt concentration, which cannot be reproduced by the fluctuations in the electrostatic field determined from MD simulations. These results point to the importance of both electrostatic and nonelectrostatic effects in the vibrational solvatochromism and dynamics in this apparently simple model system.

Predicting the solvation structure and vehicular diffusion of hydroxide ion in an anion exchange membrane using nonreactive molecular dynamics simulation

The anion exchange membranes (AEM) are generally simulated using ab initio or reactive molecular dynamics (MD) simulation approach. However, the applicability’s of these methods are still limited by computational cost, availability of force-field, transferability, etc. Empirical force-field based MD simulation can predict structure and dynamics at a lower computational cost. Considering polarizable models for hydroxide ion and water in combination with a non-polarizable model of AEM polymer, we simulate hydrated AEM. The simulated solvation structure and non-reactive dynamics are in reasonable agreement with literature. A detailed study has revealed that the diffusion of the hydroxide ion and water approximately follow hydrodynamics.

Antioxidative Action of Ellagic Acid-A Kinetic DFT Study.

Although one can find numerous studies devoted to the investigation of antioxidative activity of ellagic acid (EA) in the scientific literature, the mechanisms of its action have not yet been fully clarified. Therefore, further kinetic studies are needed to understand its antioxidative capacity completely. This work aims to reveal the underlying molecular mechanisms responsible for the antioxidative action of EA. For this purpose, its reactions with HO• and CCl3OO• radicals were simulated at physiological conditions using the quantum mechanics-based test for overall free-radical scavenging activity. The density functional theory in combination with the conductor-like polarizable continuum solvation model was utilized. With HO• radical EA conforms to the hydrogen atom transfer and radical adduct formation mechanisms, whereas sequential proton loss electron transfer mechanism is responsible for scavenging of CCl3OO• radical. In addition, compared to trolox, EA was found more reactive toward HO•, but less reactive toward CCl3OO•. The calculated rate constants for the reactions of EA with both free radicals are in a very good agreement with the corresponding experimental values.

Melting points of alkali chlorides evaluated for a polarizable and non-polarizable model.

Accurate molecular models of pure alkali halides are a prerequisite for developing transferable models of molten salts that can predict the properties of complex salt mixtures, such as those including dissolved actinide species and metal ions. Predicting the melting point of a substance represents a rigorous test of model quality. To this end, we compute the melting points of the alkali chlorides for a popular non-polarizable and polarizable model. Neither model yields more accurate predictions of the melting points across the entire family of alkali chlorides. Further calculations suggest that this may be because neither model simultaneously represents both the solid and liquid phases with sufficient accuracy across all four alkali chlorides. We find that the deviation from experiment in the model enthalpy of melting may be a good indicator of the deviation from experiment in the model melting temperature. Since the enthalpy of melting is easier to calculate in simulation than melting temperature, it may be a useful quantity to target when developing new force fields for molten salts.

A novel carbon/germanium conic structure: theoretical study using density functional theory

Complete optimization without geometry constraints and calculation of electronic properties of novel conic molecules such as $$\hbox {C}_{n}\hbox {H}_{n}\hbox {Ge}_{n}\hbox {H}_{n}$$ and $$\hbox {C}_{n}\hbox {Ge}_{n}\hbox {H}_{n}$$ , with $$n = 3{-}8$$ , was carried out with density functional theory using B3LYP and PBE1PBE functionals with 6-31 $$+$$ G(d, p) and cc-pVTZ basis sets. Calculations of formation energy showed stable and peculiar geometric and electronic properties. All carbon and germanium atoms for $$\hbox {C}_{n}\hbox {H}_{n}\hbox {Ge}_{n}\hbox {H}_{n}$$ compounds, which are $$\hbox {sp}^{\mathrm {3}}$$ -hybridized, were located in the same plane. This finding contradicts the notions of hybridization known to date. For these new molecular compounds, quantum descriptors such as electrochemical potential ( $$\mu $$ ), chemical hardness ( $$\eta $$ ), electrophilicity index ( $$\omega $$ ), dipole moment, energy gap and the shape of the molecular orbital have been calculated in addition to nucleus independent chemical shifts, polarizability and harmonic oscillator model of aromaticity which are important tools for determining the aromaticity of the studied compounds. Thus, the aim of the work is, on the one hand, to propose new stable molecular structures formed of carbon and germanium atoms, and on the other hand, to challenge our understanding of hybridization and aromaticity notion.

Electronic continuum correction without scaled charges

In recent years the “Pandora's box” of charges used in classical simulations of nonpolarizable molecular models, especially for aqueous solutions and ionic liquids, has been opened. Particularly we refer to the Electronic continuum correction (ECC) model that suggests applying scaled down charges of ions and tearing down the ‘dogma’ of identical charges used to describe the potential energy surfaces (PES) and dipole moment surface (DMS). We elaborate on both ideas and integrate them into a consistent description of ‘real’ atomic charges of water and ions, which does not necessarily need to violate the ‘dogma’. We promote ECCε approach directly incorporating the electronic polarizability into screening of electrostatic interactions, avoiding the use of scaled charges, which perplex the comparison with experiment, ab initio or polarizable models and are cumbersome for interactions with external electric or magnetic fields. We conclude that none of the existing nonpolarizable water models is fully consistent with the continuum electronic polarizability and stimulate a quest for a better model implementing ECCε ideas.

Theoretical investigations on the HOMO–LUMO gap and global reactivity descriptor studies, natural bond orbital, and nucleus-independent chemical shifts analyses of 3-phenylbenzo[d]thiazole-2(3H)-imine and its para-substituted derivatives: Solvent and substituent effects

Natural bond orbital analysis, salvation, and substituent effects of electron-releasing (–CH3, –OH) and electron-withdrawing (–Cl, –NO2, –CF3) groups at para positions on the molecular structure of synthesized 3-phenylbenzo[ d]thiazole-2(3 H)-imine and its derivatives in selected solvents (acetone, toluene, and ethanol) and in the gas phase by employing the polarizable continuum method model are studied using the M06-2x method and 6-311++G(d,p) basis set. The relative stability of the studied compounds is influenced by the possibility of intramolecular interactions between substituents and the electron donor–acceptor centers of the thiazole ring. Furthermore, atomic charges, electron density, chemical thermodynamics, energetic properties, dipole moments, and nucleus-independent chemical shifts of the studied compounds and their relative stability are considered. The dipole moment values and the highest occupied molecular orbital–lowest unoccupied molecular orbital energy gaps reveal different charge-transfer possibilities within the considered molecules. Finally, natural bond orbital analysis is carried out to picture the charge transfer between the localized bonds and lone pairs.

Unconventional Co-Existence of Insulating Nano-Regions and Conducting Filaments in Reduced SrTiO3: Mode Softening, Local Piezoelectricity, and Metallicity

Doped SrTiO3 becomes a metal at extremely low doping concentrations n and is even superconducting at n < 1020 cm−3, with the superconducting transition temperature adopting a dome-like shape with increasing carrier concentration. In this paper it is shown within the polarizability model and from first principles calculations that up to a well-defined carrier concentration nc transverse optic mode softening takes place together with polar nano-domain formation, which provides evidence of inhomogeneity and a two-component type behavior with metallicity coexisting with polarity. Beyond this region, a conventional metal is formed where superconductivity as well as mode softening is absent. For n ≤ nc the effective electron-phonon coupling follows the superconducting transition temperature. Effusion measurements, as well as macroscopic and nanoscopic conductivity measurements, indicate that the distribution of oxygen vacancies is local and inhomogeneous, from which it is concluded that metallicity stems from filaments which are embedded in a polar matrix as long as n ≤ nc.

Cluster integrals and virial coefficients for realistic molecular models.

We present a concise, general, and efficient procedure for calculating the cluster integrals that relate thermodynamic virial coefficients to molecular interactions. The approach encompasses nonpairwise intermolecular potentials generated from quantum chemistry or other sources; a simple extension permits efficient evaluation of temperature and other derivatives of the virial coefficients. We demonstrate with a polarizable model of water. We argue that cluster-integral methods are a potent yet underutilized instrument for the development and application of first-principles molecular models and methods.

Molecular Force Field Development for Aqueous Electrolytes: 2. Polarizable Models Incorporating Crystalline Chemical Potential and Their Accurate Simulations of Halite, Hydrohalite, Aqueous Solutions of NaCl, and Solubility.

The current state-of-the-art force fields (FFs) for Na+ and Cl- ions are not capable of simultaneously predicting the thermodynamic properties of the aqueous solution and the crystalline phase. This is primarily due to an oversimplification of the interaction models used but partially also due to the insufficient parametrization of the FFs. We have devised a straightforward and simple parametrization procedure for determining the ion-ion interaction parameters in complex molecular models of NaCl electrolytes which involves fitting the density, lattice energy, and chemical potential of crystalline NaCl at ambient conditions. Starting from the AH/BK3 and MAH/BK3 FFs, the parametrization approach is employed to develop a complex and accurate polarizable molecular model for the NaCl electrolyte by parametrizing the ion-ion interactions. The performance of the refined polarizable NaCl FF is assessed by evaluating the different thermodynamic and mechanical properties of the crystal, density of crystalline and molten NaCl, along with the melting temperature, properties of aqueous solutions, and the structure and stability of hydrohalite. The simulation results confirm the superiority of the refined FF in comparison with the existing state-of-the-art FFs to accurately predict a wide range of system properties in different NaCl phases, including NaCl aqueous solubility. The refined FF may find applications in the accurate simulations of NaCl electrolytes including inhomogeneous environment, phase equilibria and interfaces, and metastable states. Finally, the parametrization strategy is robust and general and can be used to devise molecular models for other electrolytes.