Van Der Waals Interaction Parameters Research Articles

Charge Scaling in Classical Force Fields for Lithium Ions in Polymers.

Polymer electrolytes are of interest for applications in energy storage. Molecular simulations of ion transport in polymer electrolytes have been widely used to study the conductivity in these materials. Such simulations have generally relied on classical force fields. A peculiar feature of such force fields has been that in the particular case of lithium ions (Li+), their charge must be scaled down by approximately 20% to achieve agreement with experimental measurements of ion diffusivity. In this work, we present first-principles calculations that serve to justify the charge-scaling factor and van der Waals interaction parameters for Li+ diffusion in poly(ethylene glycol) (PEO) with bistriflimide (TFSI-) counterions. Our results indicate that a scaling factor of 0.79 provides good agreement with DFT calculations over a relatively wide range of Li+ concentrations and temperatures, consistent with past reports where that factor was adjusted by trial and error. We also show that such a scaling factor leads to diffusivities that are in quantitative agreement with experimental measurements.

Molecular Modeling of Water-in-Salt Electrolytes: A Comprehensive Analysis of Polarization Effects and Force Field Parameters in Molecular Dynamics Simulations.

Accurate modeling of highly concentrated aqueous solutions, such as water-in-salt (WiS) electrolytes in battery applications, requires proper consideration of polarization contributions to atomic interactions. Within the force field molecular dynamics (MD) simulations, the atomic polarization can be accounted for at various levels. Nonpolarizable force fields implicitly account for polarization effects by incorporating them into their van der Waals interaction parameters. They can additionally mimic electron polarization within a mean-field approximation through ionic charge scaling. Alternatively, explicit polarization description methods, such as the Drude oscillator model, can be selectively applied to either a subset of polarizable atoms or all polarizable atoms to enhance simulation accuracy. The trade-off between simulation accuracy and computational efficiency highlights the importance of determining an optimal level of accounting for atomic polarization. In this study, we analyze different approaches to include polarization effects in MD simulations of WiS electrolytes, with an example of a Na-OTF solution. These approaches range from a nonpolarizable to a fully polarizable force field. After careful examination of computational costs, simulation stability, and feasibility of controlling the electrolyte properties, we identify an efficient combination of force fields: the Drude polarizable force field for salt ions and non-polarizable models for water. This cost-effective combination is sufficiently flexible to reproduce a broad range of electrolyte properties, while ensuring simulation stability over a relatively wide range of force field parameters. Furthermore, we conduct a thorough evaluation of the influence of various force field parameters on both the simulation results and technical requirements, with the aim of establishing a general framework for force field optimization and facilitating parametrization of similar systems.

FTIR study on the C[dbnd]O interactions of benzeneacetamide in solution

The main attention of present work is to study how benzeneacetamide interacts with other molecules in organic solvents. The frequencies of CO groups in 18 solvents were obtained by using infrared spectroscopy. The empirical parameters of the solvents as the acceptor number (AN), the van der Waals interaction parameters (SVW) and the linear solvation energy relationships (LSER) were correlated with the frequencies of carbonyl stretching vibration (ν(CO)) of benzeneacetamide to estimate the contributions in intermolecular interactions. The results showed that solvent effects on the frequencies of CO stretching vibrations of benzeneacetamide were obvious. Self-association of alkanol leads to enhancement of O–H⋯O=C hydrogen bond strength and red-shift of the ν(CO) peak. The ν(CO) of benzeneacetamide is more vulnerable to the acidity of the hydrogen bond donor of the solvent. This research contributes to a thorough understanding of the molecular interactions and microstructures in the liquid mixtures.

Thermal-FIST: A package for heavy-ion collisions and hadronic equation of state

Thermal-FIST11Thermal-FIST — Thermal, Fast and Interactive Statistical Toolkit. is a C++ package designed for convenient general-purpose physics analysis within the family of hadron resonance gas (HRG) models. This mainly includes the statistical analysis of particle production in heavy-ion collisions and the phenomenology of hadronic equation of state. Notable features include fluctuations and correlations of conserved charges, effects of probabilistic decay, chemical non-equilibrium, and inclusion of van der Waals hadronic interactions. Calculations are possible within the grand canonical ensemble, the canonical ensemble, as well as in mixed-canonical ensembles combining the canonical treatment of certain conserved charges with the grand-canonical treatment of other conserved charges. The package contains a fast thermal event generator, which generates particle yields in accordance with the HRG chemistry, and particle momenta based on the Blast Wave model. A distinct feature of this package is the presence of the graphical user interface frontend – QtThermalFIST – which is designed for fast and convenient general-purpose HRG model applications. Program summaryProgram Title:Thermal-FIST, version 1.2Program Files doi:http://dx.doi.org/10.17632/pprr8p4fkp.1Licensing provisions: GPLv3Programming language: C++External routines:Eigen template library for the linear algebra routines [1], MINUIT2 package from CERN ROOT [2], Mersenne Twister random number generator [3], Qt5 framework [4] (for the GUI only), QCustomPlot Qt widget [5] (for the GUI only)Nature of problem: The HRG model and its various modifications constitute a common framework used for modeling of the hadronic equation of state and particle production in heavy-ion collisions. Even the simplest versions of the HRG model require careful considerations of the many details, including the resonance decay feed-down, implementation of charge conservation constraints relevant for heavy-ion collisions, chemical non-equilibrium effects. A notable extra effort is required in order to treat the fluctuations and correlations of various charges , which presently are being extensively studied in the heavy-ion collision experiments and lattice QCD calculations. The inclusion of hadronic interactions, modeled by an excluded-volume (EV) or a van der Waals (vdW) type framework, additionally requires a numerical solution to a system of many transcendental equations.Solution method: The Thermal-FIST package contains a class-based library which calculates relevant HRG observables for a specified setup. The setup includes a particle list, usually to be supplied with an external file, an HRG model specification (statistical ensemble, van der Waals interaction parameters, etc.), a set of thermal parameters, and conservation laws constraints. Whenever necessary, the systems of transcendental equations are solved numerically with the Broyden’s method. The package includes a fitter for extracting thermal parameters from hadron yield data through the χ2 minimization. The HRG model based Monte Carlo event generator is a complementary feature to analytic calculations. A general-purpose thermal analysis is made maximally convenient with QtThermalFIST — a GUI frontend based on the Qt framework where all typical calculations, such as the properties of the equation of state or the thermal fits, can be straightforwardly performed.Additional comments: If the EV/vdW interactions are present, exact analytic calculations are presently only possible within the grand canonical ensemble. Approximate calculations are possible for the strangeness-canonical ensemble on the condition that strange particles form a small subsystem relative to the total system. Effects of probabilistic decays on fluctuation observables are generally included only up to the moments of the 2nd order. The only exception is the ideal HRG model in the grand canonical ensemble, where these effects are included up to the moments of the 4th order. On the other hand, the Monte Carlo event generator is not constrained by the above restrictions.

New insights about reactive red 141 adsorption onto multi–walled carbon nanotubes using statistical physics coupled with Van der Waals equation

In this communication, statistical physics models (sta–phy) coupled with the Van der Waals (VDW) state equation were employed to demonstrate insights regarding the reactive red 141 (RR 141) adsorption onto multi–walled carbon nanotubes (MWCNTs). Experimental isotherms were constructed for two types of carbon nanotubes (MWCNTs–OH and MWCNTs–COOH) at four different temperatures (298, 308, 318 and 328 K). These curves were predicted by sta–phy models coupled or not with the VDW state equation. It was demonstrated that the sta–phy coupled with VDW equation was able to predict the experimental isotherms more accurately than the other used models. Based in this approach, insights about RR 141 adsorption on the MWCNTs were presented considering the following parameters: number of molecules adsorbed at first and second site (n1 and n2), density of first and second receptor site (Nm1 and Nm2), concentration at half saturation relative to the first and second receptor site (W1 and W2) and VDW interaction parameters (a and b). The Van der Waals parameter related with the co–volume of the adsorbate molecule (b) was significant and ranged from 0.00001 to 0.00302 L mg−1.

Noble gas endohedral fullerenes, Ng@C60 (Ng=Ar, Kr): a particular benchmark for assessing the account of non-covalent interactions by density functional theory calculations

This work is dedicated to a special test, checking the capability of density functional theory computations in the account of long-range effects. The particular case of endohedral noble gas atoms in C60 fullerene puts several methodological challenges, such as the numeric problem in the balance of covalent versus non-covalent interactions. We designed a procedure based on the shifts of vibrational frequencies in C60 versus Ng@C60 couples. The energy scale of the investigated vibrations is comparable to that of the extracted van der Waals interaction parameters, achieving then a well-tempered description. A phenomenological model, based on transparent analytical formulas of the totally symmetric modes, is outlined and used to assess the computational results on series of functionals belonging to different classes (genuine forms, long-range corrected and with empiric dispersion ingredients). While the vast majority of the tested functionals undergo failures, good results are obtained for some long-range-corrected functionals (LC-BLYP and LC-wPBE), which follow the Tsuneda and Hirao’s scheme, provided that richer basis sets (with diffuse components) are used. Successes are obtained also for the Grimme B97D functional, when coupled with the D2 and D3 dispersion scheme, the results being rather independent from the basis set, as expected from the empirical nature of this type of amendment.

Progress and Prospect of Theoretical Simulation of Microporous Materials

Microporous materials, which refers to the porous materials with pores of less than 2 nm, have been widely used for heterogeneous catalysis, adsorption, separation, gas storage and other numbers of advanced applications. their high-profile application is mainly focused in the field of energy and environment research, such as the storage and separation of hydrogen, carbon dioxide and methane. according to the compositions and structures, common microporous materials include molecular sieves, porous carbon materials, metal-organic framework compounds (mop) and microporous organic polymer (mop). due to the diversity of element components and structure characteristics, the number of the microporous materials, which can be synthesized in principle, is considerably large. it is impossible to study these materials only by means of experimental methods. with the rapid development of computing power and numerical methods, the theoretical methods used in the studies of microporous materials not only provide the material properties at the molecular level, but also reveal the micro-scale experimental mechanism. therefore, it is beneficial for establishing the corresponding relationship between the material structures and their properties, leading to promoting the design and development of novel microporous materials. currently, the accurate theoretical simulations firstly calculate the intermolecular interactions between the key moiety originated from the microporous material and the target molecule through the computational method of quantum chemistry, thereby acquired the potential energy curve of the system. then the van der waals interaction parameters of the force field were fitted. based on the force field, the processes of gas adsorption in the porous materials were simulated by grand-canonical monte-carlo (gcmc) method. good agreements between gcmc simulation results and experimental data for adsorption isotherms and heats of adsorption have been observed in many studies. this paper reviews the theoretical methods recently used in the study of the various microporous materials and the latest theoretical research findings. moreover, the main problems, development prospects and the direction for future research in the study of microporous materials are pointed out.

Molecular dynamics simulation of protein crystal with polarized protein-specific force field.

Two 250 ns molecular simulations have been carried out to study the structure and dynamics of crystal toxin protein II from the scorpion Androctonus australis Hector employing the polarized protein-specific charge (PPC), as well as the standard AMBER99SB force field, to investigate the electrostatic polarization on the simulated crystal stability. Results show that under PPC, the monomers in unit cell as well as the lattice in supercell are more stable with smaller root-mean-square deviations and more accurate lattice atomic fluctuations compared with the crystallographic B-factors than under AMBER99SB force field. Most of the interactions at interfaces in the X-ray structure are quite well-preserved, underscoring the important effect of polarization on maintaining the crystal stability. However, the results also show that the hydrogen bond between Asp53 and Gln37 and the cation-π interaction between Arg56 and His64 are not stable, indicating that further optimization of force field, especially the van der Waals interaction parameters, is desired.

Hydration Free Energies of Multifunctional Nitroaromatic Compounds.

Nitroaromatic compounds (NACs) are used as energetic materials, reagents, and pesticides; however, they are potentially hazardous for the environment and human health. To predict the environmental distribution of these compounds, the vapor pressure, aqueous solubility, and Henry's law constant are important properties, as is the solvation free energy in water from which the latter two can be computed. Here, we have calculated the hydration free energies for a set of nine nitroaromatic compounds containing one, two, and three nitro groups using the expanded ensemble molecular dynamics simulation method with TIP3P water and the GAFF, CGenFF, OPLS-AA, and TraPPE force field parameters and the RESP (gas phase), CHELPG (gas phase), and CM4 (aqueous phase) partial atomic charges calculated here. Also, we have computed hydration free energies using the reported default partial atomic charges of the OPLS-AA force field and using the semiempirical AM1-BCC charges with GAFF parameters. The effect of water model flexibility on the computation of hydration free energy is examined with CGenFF/(CHELPG+SPC-Fw) model. All the force fields studied generally led to less accurate predictions with increasing numbers of nitro groups. The average unsigned errors (AUE) show that 6 of 16 force-field/(charge+water) models used perform approximately equally well in predicting measured hydration free energies: these are CGenFF/(CHELPG+TIP3P), CGenFF/(CM4+TIP3P), OPLS-AA/(CHELPG+TIP3P), OPLS-AA/(CM4+TIP3P), TraPPE-UA/(CHELPG+TIP3P), and TraPPE-UA/(CM4+TIP3P). When using the default atomic charges, the OPLS-AA force field was the most accurate, though using CHELPG and CM4 charges led to better predictions. Our analyses indicate that not only the charges but also the van der Waals interaction parameters for the nitro-group nitrogen and oxygen atoms in the force fields are partly responsible for the performance variations in predicting solvation free energies. We also compared the force field-based simulation results with the predictions from the SM6 solvation model and Abraham linear solvation energy relationship (LSER) method. With an appropriate choice of theory and basis set both for geometry optimization and computation, which unfortunately is not known a priori, the SM6 model hydration free energy predictions for the NACs are comparable to the simulation results here. The Abraham LSER predictions with descriptors obtained from the Platts method are of reasonable accuracy. A useful addition to this paper is the Supporting Information that contains a compiled and evaluated list of the hydration free energies of the NACs studied here assembled from the literature.

Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems

Atomic-scale modeling of compacted nucleic acids has the ability to reveal the inner workings of spectacular biomolecular machines, yet the outcome of such modeling efforts sensitively depends on the accuracy of the underlying computational models. Our molecular dynamics simulations of an array of 64 parallel duplex DNA revealed considerable artifacts of cation–DNA phosphate interactions in CHARMM and AMBER parameter sets: both the DNA arrangement and the pressure inside the DNA arrays were found to be in considerable disagreement with experiment. To improve the models, we fine-tuned van der Waals interaction parameters for specific ion pairs to reproduce experimental osmotic pressure of binary electrolyte solutions of biologically relevant ions. Repeating the DNA array simulations using our parameters produced results consistent with experiment. Our improved parametrization can be directly applied to molecular dynamics simulations of various charged biomolecular systems, including nucleic acids, proteins...

Computation of methodology-independent single-ion solvation properties from molecular simulations. IV. Optimized Lennard-Jones interaction parameter sets for the alkali and halide ions in water

The raw single-ion solvation free energies computed from atomistic (explicit-solvent) simulations are extremely sensitive to the boundary conditions and treatment of electrostatic interactions used during these simulations. However, as shown recently [M. A. Kastenholz and P. H. Hünenberger, J. Chem. Phys. 124, 224501 (2006); M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144103 (2010)], the application of appropriate correction terms permits to obtain methodology-independent results. The corrected values are then exclusively characteristic of the underlying molecular model including in particular the ion-solvent van der Waals interaction parameters, determining the effective ion size and the magnitude of its dispersion interactions. In the present study, the comparison of calculated (corrected) hydration free energies with experimental data (along with the consideration of ionic polarizabilities) is used to calibrate new sets of ion-solvent van der Waals (Lennard-Jones) interaction parameters for the alkali (Li(+), Na(+), K(+), Rb(+), Cs(+)) and halide (F(-), Cl(-), Br(-), I(-)) ions along with either the SPC or the SPC/E water models. The experimental dataset is defined by conventional single-ion hydration free energies [Tissandier et al., J. Phys. Chem. A 102, 7787 (1998); Fawcett, J. Phys. Chem. B 103, 11181] along with three plausible choices for the (experimentally elusive) value of the absolute (intrinsic) hydration free energy of the proton, namely, ΔG(hyd)(⊖)[H(+)] = -1100, -1075 or -1050 kJ mol(-1), resulting in three sets L, M, and H for the SPC water model and three sets L(E), M(E), and H(E) for the SPC/E water model (alternative sets can easily be interpolated to intermediate ΔG(hyd)(⊖)[H(+)] values). The residual sensitivity of the calculated (corrected) hydration free energies on the volume-pressure boundary conditions and on the effective ionic radius entering into the calculation of the correction terms is also evaluated and found to be very limited. Ultimately, it is expected that comparison with other experimental ionic properties (e.g., derivative single-ion solvation properties, as well as data concerning ionic crystals, melts, solutions at finite concentrations, or nonaqueous solutions) will permit to validate one specific set and thus, the associated ΔG(hyd)(⊖)[H(+)] value (atomistic consistency assumption). Preliminary results (first-peak positions in the ion-water radial distribution functions, partial molar volumes of ionic salts in water, and structural properties of ionic crystals) support a value of ΔG(hyd)(⊖)[H(+)] close to -1100 kJ·mol(-1).

Development of a force field for molecular simulation of the phase equilibria of perfluoromethylpropyl ether

A first step towards the development of a general, realistic potential model for perfluoroether compounds has been to parameterize a united atom model for a short chain perfluoroether perfluoromethylpropyl ether (CF3CF2CF2OCF3). The potential model takes the usual form in which separate bond bending and torsional terms describe the intramolecular interactions with the addition of van der Waals and electrostatic terms to describe the non-bonded interactions. Ab initio quantum calculations have been carried out to obtain the partial charges and intramolecular torsional and bending potentials. Phase equilibrium data were then used to optimize the van der Waals interaction parameters through Gibbs ensemble Monte Carlo simulations. The resulting model reproduces vapour-liquid equilibrium densities, the critical temperature and the critical density of perfluoromethylpropyl ether, in good agreement with those from experiment.