Lennard-Jones Parameters Research Articles

Electrical double layer in molten salts taking into account Lennard-Jones potential

Results are presented of canonical ensemble Monte Carlo simulations of molten salt electrical double layers. Electrode surface atoms and ions are modelled as soft spheres with the use of the Lennard-Jones potential. Ions and electrode atoms have the same diameter but differ in the applied energetic Lennard-Jones parameter values. The electrode surface consists of C (graphite), Hg or Pb atoms. The values of the applied parameters allow a comparison of the results obtained with those of real systems. The paper presents such results as: ion distributions, the mean electrostatic potential and differential capacitance. The differential capacitance values are collated with theoretical and experimental results. The capacitance curves obtained by simulations are flatter than experimental ones. The theoretical capacitance values, in contrast to the experimental ones, are smaller at the positive electrode potentials and this difference is due to the occurrence of chemical bonding between anions and electrode surface in experimental systems.

Data-Driven Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters.

Molecular dynamics simulations are helpful tools for a range of applications, ranging from drug discovery to protein structure determination. The successful use of this technology largely depends on the potential function, or force field, used to determine the potential energy at each configuration of the system. Most force fields encode all of the relevant parameters to be used in distinct atom types, each associated with parameters for all parts of the force field, typically bond stretches, angle bends, torsions, and nonbonded terms accounting for van der Waals and electrostatic interactions. Much attention has been paid to the nonbonded parameters and their derivation, which are important in particular due to their governance of noncovalent interactions, such as protein-ligand binding. Parametrization involves adjusting the nonbonded parameters to minimize the error between simulation results and experimental properties, such as heats of vaporization and densities of neat liquids. In this setting, determining the best set of atom types is far from trivial, and the large number of parameters to be fit for the atom types in a typical force field can make it difficult to approach a true optimum. Here, we utilize a previously described Minimal Basis Iterative Stockholder (MBIS) method to carry out an atoms-in-molecules partitioning of electron densities. Information from these atomic densities is then mapped to Lennard-Jones parameters using a set of mapping parameters much smaller than the typical number of atom types in a force field. This approach is advantageous in two ways: it eliminates atom types by allowing each atom to have unique Lennard-Jones parameters, and it greatly reduces the number of parameters to be optimized. We show that this approach yields results comparable to those obtained with the typed GAFF 1.7 force field, even when trained on a relatively small amount of experimental data.

Role of hydrogen bonding in the capture and storage of ammonia in zeolites

Ammonia is an important chemical compound used in a wide range of applications. This makes its capture, purification and recovery necessary. We combine experimental and molecular simulation techniques to identify the molecular mechanisms ruling the adsorption of ammonia in pure and high silica zeolites. To reproduce accurately the interaction between ammonia and the zeolites the development of a transferable set of Lennard-Jones parameters was needed. Adsorption isotherms were measured and also calculated using the new set of parameters for several commercial pure silica zeolites, including MFI, FAU, and LTA topologies. We found an anomalous behavior of the adsorption isotherm of ammonia in MFI, which can be explained through a monoclinic to orthorhombic structural phase transition. We also found that low concentration of extra-framework cations favors the adsorption of ammonia in these high silica zeolites. Using radial distribution functions and hydrogen bond analyses we identified ammonia clusterization as the key mechanism involved in the adsorption. Based on it, hydrophobic zeolites with large pores could be used for ammonia sequestration with lower cost than the currently used techniques.

Revisiting OPLS-AA Force Field for the Simulation of Anionic Surfactants in Concentrated Electrolyte Solutions.

Hereby, we developed a set of nonbonded parameters within all-atom optimized potentials for liquid simulations (OPLS-AA) force field for the simulation of concentrated electrolyte solutions of anionic surfactants. More specifically, the aim of this paper is to assess the performance of five sets of atomic charges calculated using different population analyses (DDEC6, CHelpG, CHelpG-SMD, RESP, and CM5), as well as the original set of charges used in the literature for sodium dodecyl sulfate (SDS) simulation. Recently, Farafonov et al. have revised the SDS OPLS-AA force field; however, we were unable to obtain the experimental rodlike micelles using this parameter set on long time scale. In fact, the initial SDS bilayer micelle adopted a rodlike shape transiently and then broke down into spherical micelles. Updating OPLS-AA force field with DDEC6, CHelpG, and CHelpG-SMD charges resulted in stable rod micelles for a long simulation time (1 μs). The atomic charges of Farafonov (taken from Shelley et al.), RESP, and CM5 could not correctly describe SDS in concentrated electrolyte solutions. Analysis of the interaction of SDS with the counterions and solvent highlights the role of a balance of the intermolecular forces that must be met to describe adequately the anionic surfactant electrolyte solutions. Further, the optimization of the SDS Lennard-Jones parameters enabled the Farafonov set to properly reproduce the experimental rod micelle. In addition, we have examined the performance of different parameters of sodium ions: the first developed based on the Kirkwood-Buff integrals (KBI) and the second developed by Joung et al. The excessive ion pairing caused by KBI parameters screens significantly SDS-water interactions, which stabilize the rod micelle. Further, a tight interaction of the Na+-SDS head group resulted in stabilization of the bilayer micelle as observed in the case of Na+ parameters developed by Joung et al.

Atomistic Mechanism of Anisotropic Heat Conduction in the Liquid Crystal 4-Heptyl-4'-cyanobiphenyl: All-Atom Molecular Dynamics.

All-atom molecular dynamics simulations were performed on 4-heptyl-4'-cyanobiphenyl (7CB) to study the mechanism of heat conduction in this nematic liquid crystal atomistically. To describe 7CB properly, the AMBER-type force field was optimized for the dihedral parameter of biphenyl and the Lennard-Jones parameters. The molecular dynamics calculation using the optimized force field well reproduced the experimental values of the isotropic-nematic phase transition temperature, density, and anisotropy of the thermal conductivity. Furthermore, the contributions of convection, intramolecular interaction, and intermolecular interaction to the thermal conductivity were determined by performing thermal conductivity decomposition analysis. According to the analysis, the contributions of convection, bond stretching, and bond bending interactions were higher in the direction parallel to the nematic director than that perpendicular to the director, which is the origin of the anisotropy in the nematic phase. This result indicates that the anisotropy is caused by well-aligned covalent bonds and high mobility parallel to the director. This quantitative description of the mechanism of heat conduction of 7CB is foreseen to provide new insights toward designing highly thermally conductive liquid-crystalline materials.

Applicability of a thermodynamic cycle approach for a force field parametrization targeting non-aqueous solvation free energies

Accurate solvation free energy ΔGsolv predictions require well parametrized force fields. In order to refit Lennard-Jones (LJ) parameters for improved ΔGsolv predictions for a variety of compound classes and chemical environments, a large number of ΔGsolv calculations is required. As the calculation of ΔGsolv is computational expensive, there is need for efficient but precise calculation methods. In this work, we focus on the computation of non-aqueous solvation free energies. We compare ΔGsolv results from highly precise reference simulations for transferring a solute from the vacuum into a condensed phase and results obtained from a thermodynamic cycle implementation. As test systems, we alter LJ parameters ε and σof widely used GAFF atom types ca, cl, n1, oh and os in various solute/solvent combinations. We examine the degree of configurational space overlap and find an impact by hydrogen bonds and the solvent accessible surface area. We conclude that the application of a thermodynamic cycle for the parametrization of force fields targeting ΔGsolv is useful if the adaptation of LJ parameters is limited to atom types in the solute or if only ε is changed.

Non-zero Lennard-Jones parameters for the Toukan–Rahman water model: more accurate calculations of the solvation free energy of organic substances

Application of a small radius of the hydrogen atom in molecular-mechanical models of hydrogen bonding improves the estimate of the solvation free energy of organic substances. At the same time, the density and evaporation heat of the bulk water vary slightly and are close to experimental values. Blind testing drug candidates in the SAMPL6 simulation competition showed that using the same Lennard-Jones hydrogen parameters for the hydroxyl, hydroxycarbonyl, amino, and amide groups is enough to predict log P octanol-water with MAE 0.67 and RMSD 0.75.

Overbinding and Qualitative and Quantitative Changes Caused by Simple Na+ and K+ Ions in Polyelectrolyte Simulations: Comparison of Force Fields with and without NBFIX and ECC Corrections.

Overbinding of ions is a common and well-known problem in classical molecular dynamics simulations. One of its main causes is the absence of electronic polarizability in the force fields. The current approaches for minimizing overbinding typically either retain the original charges and use an ad hoc readjustment of the Lennard-Jones parameters as done in the nonbonded fix (NBFIX) approach or rescale the charges using a theoretical framework. The goal in the latter is to include shielding produced by the missing electronic polarizability as done in the electronic continuum correction (ECC) approach. NBFIX and ECC are the most common corrections, and we compare their performance to the default parameterizations provided by five different commonly used biomolecular force fields, OPLS-AA/L, CHARMM27, CHARMM36m, CHARMM22*, and AMBER99SB-ILDN. As test systems, we use poly-α,l-glutamic and poly-α,l-aspartic amino acid molecules in explicit water together with Na+ and K+ counterions. We demonstrate that the different force fields yield results that are not only quantitatively but also qualitatively different. The resulting structures of the macroions depend strongly on the model for ions. NBFIX corrections alleviate the problem of overbinding, resulting in extended peptides. The ECC corrections depend nontrivially on the original underlying model, and despite being based on a theoretical framework, they cannot always solve the problem.

Self-Assembly of Phosphocholine Derivatives Using the ELBA Coarse-Grained Model: Micelles, Bicelles, and Reverse Micelles.

The ELBA coarse-grained force field was originally developed for lipids, and its water model is described as a single-site Lennard-Jones particle with electrostatics modeled by an embedded point-dipole, while other molecules in this force field have a three (or four)-to-one mapping scheme. Here, ELBA was applied to investigate the self-assembly processes of dodecyl-phosphocholine (DPC) micelle, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/1,2-dihexaoyl-sn-glycero-3-phosphocholine (DPPC/DHPC) bicelles, and DPPC/cyclohexane/water reverse micelles through coarse-grained molecular dynamics (MD) simulations. New parameters were obtained using a simplex algorithm-based calibration procedure to determine the Lennard-Jones parameters for cyclohexane, dodecane, and cyclohexane-dodecane cross-interactions. Density, self-diffusion coefficient, surface tension, and mixture excess volume were found to be in fair agreement with experimental data. These new parameters were used in the simulations, and the obtained structures were analyzed for shape, size, volume, and surface area. Except for the shape of DPC micelles, all other properties match well with available experimental data and all-atom simulations. Remarkably, in agreement with experiments the rodlike shape of the DPPC reverse micelle is well described by ELBA, while all-atom data in the literature predicts a disclike shape. To further check the consistency of the force field in reproducing the correct shapes of reverse micelles, additional simulations were performed doubling the system size. Two distinct reverse micelles were obtained both presenting the rodlike shape and correct aggregation number.

Adsorption-Induced Expansion of Graphene Oxide Frameworks: Observation by in Situ Neutron Diffraction.

We have investigated adsorption-induced deformation in graphene oxide framework materials (GOFs) using neutron diffraction at sample pressures up to 140 bar. GOFs, made by the solvothermal reaction of graphite oxide and benzene-1,4-diboronic acid, are a suitable candidate for deformation studies due to their narrow (∼1 nm), monodispersed, slit-shaped pores whose width can be measured by diffraction techniques. We have observed, in situ, a monotonic expansion of the slit width with increasing pressure upon adsorption of xenon, methane, and hydrogen under supercritical conditions. The expansion of ∼4% observed for xenon at a pressure of 48 bar is the largest deformation yet reported for supercritical adsorption on a carbonaceous material. We find that the expansion of the three gases can be mapped onto a common curve based solely on their Lennard-Jones parameters, in a manner similar to a law of corresponding states.

Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins.

Cation-π interactions are noncovalent interactions between a π-electron system and a positively charged ion that are regarded as a strong noncovalent interaction and are ubiquitous in biological systems. Similarly, though less studied, anion-ring interactions are present in proteins along with in-plane interactions of anions with aromatic rings. As these interactions are between a polarizing ion and a polarizable π system, the accuracy of the treatment of these interactions in molecular dynamics (MD) simulations using additive force fields (FFs) may be limited. In the present work, to allow for a better description of ion-π interactions in proteins in the Drude-2013 protein polarizable FF, we systematically optimized the parameters for these interactions targeting model compound quantum mechanical (QM) interaction energies with atom pair-specific Lennard-Jones parameters along with virtual particles as selected ring centroids introduced to target the QM interaction energies and geometries. Subsequently, MD simulations were performed on a series of protein structures where ion-π pairs occur to evaluate the optimized parameters in the context of the Drude-2013 FF. The resulting FF leads to a significant improvement in reproducing the ion-π pair distances observed in experimental protein structures, as well as a smaller root-mean-square differences and fluctuations of the overall protein structures from experimental structures. Accordingly, the optimized Drude-2013 protein polarizable FF is suggested for use in MD simulations of proteins where cation-π and anion-ring interactions are critical. © 2019 Wiley Periodicals, Inc.

Pitfalls of the Martini Model

The computational and conceptual simplifications realized by coarse-grain (CG) models make them a ubiquitous tool in the current computational modeling landscape. Building block based CG models, such as the Martini model, possess the key advantage of allowing for a broad range of applications without the need to reparametrize the force field each time. However, there are certain inherent limitations to this approach, which we investigate in detail in this work. We first study the consequences of the absence of specific cross Lennard-Jones parameters between different particle sizes. We show that this lack may lead to artificially high free energy barriers in dimerization profiles. We then look at the effect of deviating too far from the standard bonded parameters, both in terms of solute partitioning behavior and solvent properties. Moreover, we show that too weak bonded force constants entail the risk of artificially inducing clustering, which has to be taken into account when designing elastic network models for proteins. These results have implications for the current use of the Martini CG model and provide clear directions for the reparametrization of the Martini model. Moreover, our findings are generally relevant for the parametrization of any other building block based force field.

Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc(II)-Binding Residues in Sites with Four Protein Ligands.

We developed and validated a novel force field in the context of the AMBER parameterization for the simulation of zinc(II)-binding proteins. The proposed force field assumes nonbonded spherical interactions between the central zinc(II) and the coordinating residues. A crucial innovative aspect of our approach is to account for the polarization effects of the cation by redefining the atomic charges of the coordinating residues and an adjustment of Lennard-Jones parameters of Zn-interacting atoms to reproduce mean distance distributions. The optimal transferable parametrization was obtained by performing accurate quantum mechanical calculations on a training set of high-quality protein structures, encompassing the most common folds of zinc(II) sites. The addressed sites contain a zinc(II) ion tetra-coordinated by histidine and cysteine residues and represent about 70% of all physiologically relevant zinc(II) sites in the Protein Data Bank. Molecular dynamics simulations with explicit solvent, carried out on several zinc(II)-binding proteins not included in the training set, show that our model for zinc(II) sites preserves the tetra-coordination of the metal site with remarkable stability, yielding zinc(II)-X mean distances similar to experimental data. Finally, the model was tested by evaluating the zinc(II)-binding affinities, using the alchemical free energy perturbation approach. The calculated dissociation constants correlate satisfactorily with the experimental counterpart demonstrating the validity and transferability of the proposed parameterization for zinc(II)-binding proteins.

Parameterization of Molybdenum Disulfide Interacting with Water Using the Free Energy Perturbation Method.

Water contact angles (WCA) are often used to parametrize force field parameters of novel 2D nanomaterials, such as molybdenum disulfide (MoS2), which has emerged as a promising nanomaterial in many biomedical applications due to its unique and impressive properties. However, there is a wide range of water-MoS2 contact angles in the literature depending on the aging process on the surface of a MoS2 nanosheet and/or substrate material. In this study, we revisit and optimize existing parameters for the basal plane of MoS2 with two popular water models, TIP3P and SPC/E, using the wide range of WCAs from various experiments. We develop and deploy the free energy perturbation method for parametrizing MoS2 with experimentally determined WCAs for both fresh and aged surfaces. Energy decomposition analysis on the simulation trajectories reveals that MoS2-water interaction is dominated by van der Waals interaction, which mainly comes from the top layer of MoS2. We conclude that to describe both fresh and aged MoS2 surfaces it is convenient to only adjust the Lennard-Jones parameter εS (the depth of the potential well of a sulfur atom), which displays a surprisingly linear correlation with WCAs.

Development of Nonbonded Models for Metal Cations Using the Electronic Continuum Correction

The parametrization of classical nonbonded models of metal ions has been widely addressed in the recent years. Despite the continuous development of novel and more physically inspired functional forms, the 12-6 Lennard-Jones plus Coulomb potential is still the most adopted force field in molecular dynamics (MD) codes, owing to its simple form and easy implementation. However, due to the integer formal charge, unpolarizable force fields of ions may suffer from overestimated interatomic electrostatic interactions, leading to nonphysical clustering or repulsion between such full charges. The electronic continuum correction (ECC) can fix this problem through a simple inclusion of solvent polarization effects via ionic charge rescaling. In this work, the development of novel nonbonded models for mono, divalent, and highly charged metal ions is presented. For each metal species, the ionic charge has been scaled, according to the ECC. Lennard-Jones parameters have been optimized using experimental structural and thermodynamic properties as target quantities. Performances of the proposed models are discussed and compared with the literature data, while transferability attitudes among different and well-known water models are evaluated. © 2019 Wiley Periodicals, Inc.

Simulating Surfactant–Iron Oxide Interfaces: From Density Functional Theory to Molecular Dynamics

Understanding the behavior of surfactant molecules on iron oxide surfaces is important for many industrial applications. Molecular dynamics (MD) simulations of such systems have been limited by the absence of a force field (FF), which accurately describes the molecule-surface interactions. In this study, interaction energies from density functional theory (DFT) + U calculations with a van der Waals functional are used to parameterize a classical FF for MD simulations of amide surfactants on iron oxide surfaces. The original FF, which was derived using mixing rules and surface Lennard-Jones (LJ) parameters developed for nonpolar molecules, was shown to significantly underestimate the adsorption energy and overestimate the equilibrium adsorption distance compared to DFT. Conversely, the optimized FF showed excellent agreement with the interaction energies obtained from DFT calculations for a wide range of surface coverages and molecular conformations near to and adsorbed on α-Fe2O3(0001). This was facilitated through the use of a Morse potential for strong chemisorption interactions, modified LJ parameters for weaker physisorption interactions, and adjusted partial charges for the electrostatic interactions. The original FF and optimized FF were compared in classical nonequilibrium molecular dynamics simulations of amide molecules confined between iron oxide surfaces. When the optimized FF was employed, the amide molecules were pulled closer to the surface and the orientation of the headgroups was more similar to that observed in the DFT calculations. The optimized FF proposed here facilitates classical MD simulations of anhydrous amide-iron oxide interfaces in which the interactions are representative of accurate DFT calculations.

Refined Empirical Force Field to Model Protein-Self-Assembled Monolayer Interactions Based on AMBER14 and GAFF.

Understanding protein interaction with material surfaces is important for the development of nanotechnological devices. The structures and dynamics of proteins can be studied via molecular dynamics (MD) if the protein-surface interactions can be accurately modeled. To answer this question, we computed the adsorption free energies of peptides (representing eleven different amino acids) on a hydrophobic self-assembled monolayer (CH3-SAM) and compared them to the benchmark experimental data set. Our result revealed that existing biomolecular force fields, GAFF and AMBER ff14sb, cannot reproduce the experimental peptide adsorption free energies by Wei and Latour (Langmuir, 2009, 25, 5637-5646). To obtain the improved force fields, we systematically tuned the Lennard-Jones parameters of selected amino acid sidechains and the functional group of SAM with repeated metadynamics and umbrella sampling simulations. The final parameter set has yielded a significant improvement in the free energy values with R = 0.83 and MSE = 0.65 kcal/mol. We applied the refined force field to predict the initial adsorption orientation of lysozyme on CH3-SAM. Two major orientations-face-down and face-up-were predicted. Our analysis on the protein structure, solvent accessible surface area, and binding of native ligand NAG3 suggested that lysozyme in the face-up orientation can remain active after initial adsorption. However, because of its weaker affinity (ΔΔG = 7.86 kcal/mol) for the ligand, the bioactivity of the protein is expected to reduce. Our work facilitates the use of MD for the study of protein-SAM systems. The refined force field compatible with GROMACS is available at https://cbbio.cis.um.edu.mo/software/SAMFF .

Are Explicit Solvent Models More Accurate than Implicit Solvent Models? A Case Study on the Menschutkin Reaction.

In this work, contemporary quantum mechanical (QM) implicit solvent models (SMD, SM12, and COSMO-RS) and a molecular mechanical (MM) explicit solvent model were used to predict the aqueous free energy barrier of a simple Menschutkin reaction (NH3 + CH3Cl). Surprisingly, the explicit solvent approach performed the worst, while the implicit solvent models yielded reasonably accurate values that are in accord with available experimental data. The origin of the large error in the explicit solvent model was due to the use of a fixed set of Lennard-Jones parameters during the free energy perturbation (FEP) calculations. Further analyses indicate that M06-2X/6-31+G(d,p) yielded solute-solvent interaction energies that are in good agreement with benchmark DLPNO-CCSD(T)/CBS values. When end-state MM to M06-2X/6-31+G(d,p) corrections were added using FEP, it significantly improved the accuracy of the explicit solvent MM result and demonstrated that the accuracy of these models may be systematically improved with end-state corrections based on a validated QM level of theory.

Prediction of experimental properties of CO2: improving actual force fields.

Most of the existing classical CO2 models fail to reproduce some or many experimental properties such as surface tension, vapor pressure, density, and dielectric constant at difference thermodynamic conditions. Therefore, it we propose a new computational model to capture better structural, dynamical, and thermodynamic properties for CO2. By scaling the Lennard-Jones parameters and point charges; three target properties, static dielectric constant, surface tension, and density, were used to fit actual experimental data. Moreover, by constructing a flexible model, effects of polarization might be included by variations of the dipole moment. Several tests were carried out in terms of the vapor-liquid equilibria, surface tensions, and saturated pressures showing good agreement with experiments. Dynamical properties were also studied, such as diffusion coefficients and viscosities at different pressures, and good trends were obtained with experimental data.

Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects.

Atomistic biomolecular simulations predominantly utilize additive force fields (FF), where the electrostatic potential is modeled by fixed point charges. Among other consequences, the lack of polarizability in these models undermines the balance of hydrophilic/hydrophobic nonbonded interactions. Simulations of water/alkane systems using the TIP3P water model and CHARMM36 parameters reveal a 1 kcal/mol overestimate of the experimental transfer free energy of water to hexadecane; more recent optimized water models (SPC/E, TIP4P/2005, TIP4P-Ew, TIP3P-FB, TIP4P-FB, OPC, TIP4P-D) overestimate this transfer free energy by approximately 2 kcal/mol. In contrast, the polarizable SWM4-NDP and SWM6 water models reproduce experimental values to within statistical error. As an alternative to explicitly modeling polarizability, this paper develops an efficient automated workflow to optimize pair-specific Lennard-Jones parameters within an additive FF. Water/hexadecane is used as a prototype and the free energy of water transfer to hexadecane as a target. The optimized model yields quantitative agreement with the experimental transfer free energy and improves the water/hexadecane interfacial tension by 6%. Simulations of five different lipid bilayers show a strong increase of water permeabilities compared to the unmodified CHARMM36 lipid FF which consistently improves match with experiment: the order-of-magnitude underestimate for monounsaturated bilayers is rectified and the factor of 2.8-4 underestimate for saturated bilayers is turned into a factor of 1.5-3 overestimate. While agreement with experiment is decreased for the diffusion constant of water in hexadecane, alkane transfer free energies, and the bilayers' area per lipid, the method provides a permeant-specific route to achieve a wide range of heterogeneous observables via rapidly optimized pairwise parameters.