Optimized Potentials For Liquid Simulations-All Atom Research Articles

Effect of scaled ionic charges on the freezing point depression of aqueous CaCl2 solution

We examine the performance of two force fields, OPLS-AA (Optimized Potentials for Liquid Simulations - All Atom) using full ionic charges, and Madrid-2019 using scaled ionic charges, in predicting the freezing point depression of aqueous CaCl2 solutions across concentrations ranging from 5 to 30 wt%. The direct coexistence method is employed to characterize the phase transformation mechanism. Our predictions corroborate that the Madrid-2019 force field exhibits predictive consistency with experimental measurements relative to OPLS-AA. The dissimilarities in the equilibrium properties, such as diffusion coefficients, hydration structures, and densities, underscore the advantages in the ion-water and ion-ion interaction mechanisms described by Madrid-2019 force field.

Molecular Dynamics Simulation to Evaluate the Stability of Tetra-n-butyl Ammonium/Phosphonium Bromide Semiclathrate Hydrates in the Presence and Absence of Methane, Carbon Dioxide, Methanol, and Ethanol Molecules

Stability of tetra-n-butyl ammonium bromide (TBAB) and tetra-n-butyl phosphonium bromide (TBPB) semiclathrate hydrates with a hydration number of 38 is studied by the molecular dynamics (MD) simulation in the absence and presence of methane, carbon dioxide, methanol, and ethanol molecules. All of the simulation runs are performed under NVT (constant number of atoms, volume, and temperature) and NPT (constant number of atoms, pressure, and temperature) conditions using optimized potentials for liquid simulations-all-atom (OPLS-AA) force field with nonpolarizable water models (including SPC, TIP3P, TIP4P, and TIP4P/Ice), where the operating conditions include a temperature range of 250–350 K and pressures of 0.1 and 50 MPa. The potential energy and structural analysis, mean square displacement (MSD), diffusion coefficient, radial distribution function (RDF), lattice parameter, and the average number of hydrogen bonds between water–water molecules are evaluated by employing MD strategy. According to the potential energy results, the order for the water models in both TBAB and TBPB hydrate stabilities is as follows: TIP4P/Ice > TIP4P ≈ SPC > TIP3P. This order agrees well with the previous studies of gas hydrates and ices. In the absence and presence of methane and carbon dioxide guest molecules, the height of the peaks in the RDF of oxygen–oxygen atoms decreases with lowering pressure and increasing temperature; greater MSD, diffusion coefficient, and lattice parameter values are also achieved. Thus, in the absence and/or presence of guest gas molecules, the stability of TBAB and TBPB hydrate cages decreases with increasing temperature and reducing pressure. A good match is noticed between the results of MD simulation and previous experimental and theoretical studies, confirming the accuracy and validation of the simulation method. Reduction of the hydrogen bond balance between water molecules and formation of new hydrogen bonds between the water and the hydroxyl groups of methanol and/or ethanol molecules in the cages indicate that methanol and ethanol molecules have an inhibitory effect on TBAB and TBPB hydrates. Due to different hydrophilic versus hydrophobic behaviors of alcohols, the extent of disruption of hydrogen bonds between water–water molecules of TBAB and TBPB hydrates in the presence of methanol is larger than that in the presence of ethanol, which is consistent with the MD simulation results of clathrate hydrate. This study can help to further understand the semiclathrate hydrate stability or dissociation conditions at a molecular scale for better design and operation of corresponding processes.

Molecular Dynamics Study of CO2 Phase Change Transport in the Near-Critical Region: Model Parameter Optimization

The technical development of supercritical CO2, energy systems, CO2 capture, and other applications has become a hot topic in recent years. Therefore, molecular dynamics simulation (MD) of CO2, especially the investigation at the CO2 supercritical region is urgently needed. This study focused on the optimization of common CO2 potential model EPM2 (elementary physical model—2) combined MD forcefield OPLS-AA (optimized potentials for liquid simulations—all atom) and CHARMM (chemistry at Harvard macromolecular mechanics for MD simulation). Through adjusting angle parameters according to EPM2, vapor-liquid equilibrium curve, critical point and supercritical region could be well corresponding with experiments, which can be more accurate than previous approaches. The simulated results using 179.63° in OPLS-AA forcefield can not only correspond to supercritical phase of near-critical region (within ±10% error range under CO2 is at 468 kg/m3, 304.2–320 K, 7.2–10.0 MPa), but also be consistent with actual CO2 properties in gas phase of near-critical region (temperature range can reach 304.2–350 K while the density scope can reach 15–168 kg/m3). Besides, optimized potential model also has a certain reliability on the investigation of CO2 diffusion properties. The values simulated have the same order of magnitude as literature values, especially simulated diffusion coefficient values at gas phase. The CO2 property of heat capacity is also simulated, and the errors are within ±15%. That is to say, the optimized CO2 potential parameter also has a certain accuracy to analyze CO2 heat transfer. The angle value optimized in this study may be useful for the fundamental understanding of the supercritical state and it can well be applied in the further investigation of CO2 systems.

Molecular dynamics simulation of nonisothermal crystallization of a single polyethylene chain and short polyethylene chains based on OPLS force field

Abstract Molecular dynamics simulations on the nonisothermal crystallization of a single polyethylene chain and short polyethylene chains based on the all-atom model and optimized potentials for liquid simulations-all atom (OPLS-AA) force field are conducted in this article. Four all-atom single chain models with different chain lengths (C1000, C2000, C3000, and C4000) and four all-atom short chain models with the same chain length and different number of chains (2C500, 4C500, 6C500, and 8C500) are constructed. The collapse process at a high temperature of 600 K and the nonisothermal crystallization process with different cooling rates at the temperature range of 600–300 K are simulated. Roles of chain length, number of chains, cooling rate on the potential energy, van der Waals (V dw) energy, radius of gyration, root mean square deviation, and crystallinity are explored. By comparing with the existing results obtained by the united atom model, the validity and accuracy of this study are proved. Results show that in the collapse process, the chain length is the major factor, whereas the cooling rate has the greatest influence during the nonisothermal crystallization process. As the cooling rate decreases, a “platform” appeared in the V dw energy curve, which has a profound impact on the crystallization.

Investigation of thermocapillary migration of nanodroplets using molecular dynamics

Molecular dynamics is used to investigate the thermocapillary motion of a water nanodroplet suspended in benzene subjected to a constant temperature gradient. This framework lets us identify the average behavior of the fluid particles by revealing their mean evolution. We connect such statistics to the behavior of the temporally evolving nanodroplet, thereby providing a microphysical foundation to existing macroscopic models that rely on the assumption of continuum. It is shown that, despite the significant Brownian effects, the droplet exhibits the macrophysical expected behavior, i.e., it migrates toward the direction of the imposed temperature gradient. Thermophoretic effects are negligible and the functional relationships involved in such a process well resemble those of available analytical results. Additionally, we provide molecular dynamics calculations of the viscosity, thermal conductivity, and interfacial tension of benzene [using the Optimized Potentials for Liquid Simulations—All Atom (OPLSAA) molecular model] and water using the Transferable Intermolecular Potential with 4 Points (TIP4P) model at different temperatures and pressures. These findings will serve as a good reference for future simulations of similar molecular models.

Insight into structural properties of polyethylene glycol monolaurate in water and alcohols from molecular dynamics studies.

By means of molecular dynamics (MD) simulations, we explored the structural properties of polyethylene glycol monolaurate (PEGML) in water and in various aliphatic alcohols (methanol, ethanol, 2-propanol, 2-butanol, tert-butanol, and 1-pentanol). The PEGML and the alcohols were simulated using the optimized potentials for liquid simulations, all-atom (OPLS-AA) force field and water using the extended simple point charge (SPC/E) model. From the isothermal-isobaric (NPT, constant number of particles, constant pressure, and constant temperature) ensemble, we extracted the densities from the simulations and compared them with those from experimental results in order to confirm the validity of the selected force fields. The densities from MD simulations are in good agreement with the experimental values. To gain more insight into the nature of interactions between the PEGML and the solvent molecules, we analyzed the hydrogen-bonds, the electrostatic (Coulomb) interactions, and the van der Waals (Lennard-Jones) interaction energies extracted from MD simulations. The results were further strengthened by computing the solvation free energy by employing the free energy perturbation (FEP) approach. In this method, the free energy difference was computed by using the Bennet Acceptance Ratio (BAR) method. Moreover, the radial distribution functions were analyzed in order to gain more understanding of the solution behavior at the molecular level.

Solvation free energy of light alkanes in polar and amphiphilic environments

Computer simulations of molecular models are powerful technique that have improved the under- standing of many biochemical phenomena. The method is frequently applied to study the motions of biological macromolecules such as protein and nucleic acids, which can be useful for interpreting the results of certain biophysical experiments. In this work, we have estimated the solvation free energy for light alkane (methane, ethane, propane and n-butane) dissolved in water and methanol respectively over a broad range of temperatures, from 275 K to 375 K, using molecular dynamics simulations. The alkane (methane, ethane, propane and n-butane), and methanol molecules are described by the OPLS-AA (Optimized Potentials for Liquid Simulations-All Atom) potential, while water is modeled by TIP3P (Transferable Intermolecular Potential with 3-Points) model. We have used the free energy perturbation method (Bennett Acceptance Ratio (BAR) method) for the calculation of free energy of solvation. The estimated values of solvation free energy of alkane in the corresponding solvents agree well with the available experimental data.BIBECHANA 16 (2019) 91-104

Perfluoropolyethers: Development of an All-Atom Force Field for Molecular Simulations and Validation with New Experimental Vapor Pressures and Liquid Densities.

A force field for perfluoropolyethers (PFPEs) based on the general optimized potentials for liquid simulations all-atom (OPLS-AA) force field has been derived in conjunction with experiments and ab initio quantum mechanical calculations. Vapor pressures and densities of two liquid PFPEs, perfluorodiglyme (CF3-O-(CF2-CF2-O)2-CF3) and perfluorotriglyme (CF3-O-(CF2-CF2-O)3-CF3), have been measured experimentally to validate the force field and increase our understanding of the physical properties of PFPEs. Force field parameters build upon those for related molecules (e.g., ethers and perfluoroalkanes) in the OPLS-AA force field, with new parameters introduced for interactions specific to PFPEs. Molecular dynamics simulations using the new force field demonstrate excellent agreement with ab initio calculations at the RHF/6-31G* level for gas-phase torsional energies (<0.5 kcal mol-1 error) and molecular structures for several PFPEs, and also accurately reproduce experimentally determined densities (<0.02 g cm-3 error) and enthalpies of vaporization derived from experimental vapor pressures (<0.3 kcal mol-1). Additional comparisons between experiment and simulation show that polyethers demonstrate a significant decrease in enthalpy of vaporization upon fluorination unlike related molecules (e.g., alkanes and alcohols). Simulation suggests this phenomenon is a result of reduced cohesion in liquid PFPEs due to a reduction in localized associations between backbone oxygen atoms and neighboring molecules.

The diffusion behavior and capacitance of tetraethylammonium/tetrafluoroborate ions in acetonitrile with different molar concentrations: a molecular dynamics study

A molecular dynamics (MD) simulation with the optimized potentials for liquid simulations-all atom (OPLS-AA) force field was carried out to investigate the dynamic behaviors of organic electrolyte molecules between a graphite cathode and anode.

Molecular dynamics analysis of the effect of electronic polarization on the structure and single-particle dynamics of mixtures of ionic liquids and lithium salts.

We report a molecular dynamics study on the effect of electronic polarization on the structure and single-particle dynamics of mixtures of the aprotic ionic liquid 1-ethyl-3-methylimidazolium bis-(trifluoromethylsulfonyl)-imide ([EMIM][TFSI]) doped with a lithium salt with the same anion at 298 K and 1 bar. In particular, we analyze the effect of electron density fluctuations on radial distribution functions, velocity autocorrelation functions, cage correlation functions, mean-squared displacements, and vibrational densities of states, comparing the predictions of the quantum-chemistry-based Atomistic Polarizable Potential for Liquids, Electrolytes, & Polymers (APPLE&P) with those of its nonpolarizable version and those of the standard non-polarizable Optimized Potentials for Liquid Simulations-All Atom (OPLS-AA). We found that the structure of the mixture is scarcely modified by the fluctuations in electron charge of their constituents, but their transport properties are indeed quite drastically changed, with larger mobilities being predicted for the different species in the bulk mixtures with the polarizable force field. Specifically, the mean-squared displacements are larger for the polarizable potentials at identical time intervals and the intermediate subdiffusive plateaus are greatly reduced, so the transition to the diffusive regime takes place much earlier than in the non-polarizable media. Moreover, the correlations of the added cations inside their cages are weakened out earlier and their vibrational densities of states are slightly red-shifted, reflecting the weakening effect of the electronic polarization on the Coulomb coupling in these dense ionic media. The comparison of OPLS-AA with non-polarizable APPLE&P indicates that adding polarization to OPLS-AA is not sufficient to achieve results close to experiments.

Parameterization and optimization of the menthol force field for molecular dynamics simulations.

Menthol’s various biological properties render it a useful component for medical and cosmetological applications, while its three centers of asymmetry mean that it can be used in a range of organic reactions. Menthol-substituted ionic liquids (ILs) have been found to exhibit promising antimicrobial and antielectrostatic properties, as well as being useful in organic catalysis and biochemical studies. However, so far, a force field designed and validated specifically for the menthol molecule has not been constructed. In the present work, the validation and optimization of force field parameters with regard to the ability to reproduce the macroscopic properties of menthol is presented. The set of optimized potentials for liquid simulations all atom (OPLS-AA) compatible parameters was tested and carefully tuned. The refinement of parameters included fitting of partial atomic charges, optimization of Lennard-Jones parameters, and recalculation of the dihedral angle parameters needed to reproduce quantum energy profiles. To validate the force field, a variety of physicochemical properties were calculated for liquid menthol. Both thermodynamic and kinetic properties were taken into account, including density, surface tension, enthalpy of vaporization, and shear viscosity. The obtained force field was proven to accurately reproduce the properties of the investigated compound while being fully compatible with the OPLS-AA force field.Electronic supplementary materialThe online version of this article (doi:10.1007/s00894-016-3082-1) contains supplementary material, which is available to authorized users.

Molecular Dynamics Simulation Study of the Selectivity of a Silica Polymer for Ibuprofen.

In the past few years, the sol-gel polycondensation technique has been increasingly employed with great success as an alternative approach to the preparation of molecularly imprinted materials (MIMs). The main aim of this study was to study, through a series of molecular dynamics (MD) simulations, the selectivity of an imprinted silica xerogel towards a new template—the (±)-2-(P-Isobutylphenyl) propionic acid (Ibuprofen, IBU). We have previously demonstrated the affinity of this silica xerogel toward a similar molecule. In the present study, we simulated the imprinting process occurring in a sol-gel mixture using the Optimized Potentials for Liquid Simulations-All Atom (OPLS-AA) force field, in order to evaluate the selectivity of this xerogel for a template molecule. In addition, for the first time, we have developed and verified a new parameterisation for the Ibuprofen® based on the OPLS-AA framework. To evaluate the selectivity of the polymer, we have employed both the radial distribution functions, interaction energies and cluster analyses.

Quantum-Chemical and Molecular Dynamics Study of M+[TOTO]−(M = Li, Na, K) Ionic Liquids

Quantum-chemical calculations and classical molecular dynamics simulations with the Optimized Potentials for Liquid Simulations-All Atom (OPLS-AA) force field are presented for ionic liquids based on 2,5,8,11-tetraoxatridecan-13-oate anion (TOTO) and alkali cations (Li, Na, K). Complexation energies decrease with increasing cation radius from Li to K. Cation interactions with carboxylate oxygen atoms are preferred over complexation to ether oxygens. Cross-linking occurs in the structure of the liquid because of interactions of multiple metal ions with carboxylate oxygen atoms from multiple TOTO anions. Anticorrelated motion of ions of the same charge is an important factor decreasing conductivity of the liquid. Results of modeling agree with available experimental data for Na-TOTO.

QuanPol: A full spectrum and seamless QM/MM program

The quantum chemistry polarizable force field program (QuanPol) is implemented to perform combined quantum mechanical and molecular mechanical (QM/MM) calculations with induced dipole polarizable force fields and induced surface charge continuum solvation models. The QM methods include Hartree-Fock method, density functional theory method (DFT), generalized valence bond theory method, multiconfiguration self-consistent field method, Møller-Plesset perturbation theory method, and time-dependent DFT method. The induced dipoles of the MM atoms and the induced surface charges of the continuum solvation model are self-consistently and variationally determined together with the QM wavefunction. The MM force field methods can be user specified, or a standard force field such as MMFF94, Chemistry at Harvard Molecular Mechanics (CHARMM), Assisted Model Building with Energy Refinement (AMBER), and Optimized Potentials for Liquid Simulations-All Atom (OPLS-AA). Analytic gradients for all of these methods are implemented so geometry optimization and molecular dynamics (MD) simulation can be performed. MD free energy perturbation and umbrella sampling methods are also implemented.

A theoretical study of N–H ··· π H-bond interaction of pyrrole: from clusters to the liquid

The N–H ··· π H-bond interactions of clusters and liquid formed by pyrrole molecules were investigated by Quantum Mechanics (QM) and classical Molecular Dynamics (MD), respectively. Based on the optimized geometry at the B97-D/aug-cc-pVTZ level of theory including dispersion correction, the nature and the origin of N–H ··· π H-bond interactions were unveiled by atoms in molecules (AIM), natural bond orbital (NBO), and energy decomposition analysis (EDA). Among them, the AIM analysis gives evidence to the presence of N–H ··· π H-bond interactions, the NBO examination reveals that π → σ* donor-acceptor orbital interaction is of great importance. EDA study indicates that N–H ··· π interactions are governed by the electrostatic and dispersion term. Meanwhile, MD simulation with OPLS-AA (optimized potentials for liquid simulations all-atom) was applied to study the pure liquid pyrrole at different temperature. The results confirm the existence of the N–H ··· π H-bond in the pure liquid pyrrole, and further characterized the structures of this H-bond which is somewhat different to the clusters.

Molecular dynamics simulations of triflic acid and triflate ion/water mixtures: A proton conducting electrolytic component in fuel cells

Triflic acid is a functional group of perflourosulfonated polymer electrolyte membranes where the sulfonate group is responsible for proton conduction. However, even at extremely low hydration, triflic acid exists as a triflate ion. In this work, we have developed a force-field for triflic acid and triflate ion by deriving force-field parameters using ab initio calculations and incorporated these parameters with the Optimized Potentials for Liquid Simulations - All Atom (OPLS-AA) force-field. We have employed classical molecular dynamics (MD) simulations with the developed force field to characterize structural and dynamical properties of triflic acid (270-450 K) and triflate ion/water mixtures (300 K). The radial distribution functions (RDFs) show the hydrophobic nature of CF(3) group and presence of strong hydrogen bonding in triflic acid and temperature has an insignificant effect. Results from our MD simulations show that the diffusion of triflic acid increases with temperature. The RDFs from triflate ion/water mixtures shows that increasing hydration causes water molecules to orient around the SO(3)(-) group of triflate ions, solvate the hydronium ions, and other water molecules. The diffusion of triflate ions, hydronium ion, and water molecules shows an increase with hydration. At λ = 1, the diffusion of triflate ion is 30 times lower than the diffusion of triflic acid due to the formation of stable triflate ion-hydronium ion complex. With increasing hydration, water molecules break the stability of triflate ion-hydronium ion complex leading to enhanced diffusion. The RDFs and diffusion coefficients of triflate ions, hydronium ions and water molecules resemble qualitatively the previous findings using per-fluorosulfonated membranes.

Optimal scaling factors for CM1 and CM3 atomic charges in RM1‐based aqueous simulations

Scaling factors for atomic charges derived from the RM1 semiempirical quantum mechanical wavefunction in conjunction with CM1 and CM3 charge models have been optimized by minimizing errors in absolute free energies of hydration, ΔG(hyd) , for a set of 40 molecules. Monte Carlo statistical mechanics simulations and free energy perturbation theory were used to annihilate the solutes in gas and in a box of TIP4P water molecules. Lennard-Jones parameters from the optimized potentials for liquid simulations-all atom (OPLS-AA) force field were utilized for the organic compounds. Optimal charge scaling factors have been determined as 1.11 and 1.14 for the CM1R and CM3R methods, respectively, and the corresponding unsigned average errors in ΔG(hyd) relative to experiment were 2.05 and 1.89 kcal/mol. Computed errors in aniline and two derivatives were particularly large for RM1 and their removal from the data set lowered the overall errors to 1.61 and 1.75 kcal/mol for CM1R and CM3R. Comparisons are made to the AM1 method which yielded total errors in ΔG(hyd) of 1.50 and 1.64 kcal/mol for CM1A*1.14 and CM3A*1.15, respectively. This work is motivated by the need for a highly efficient yet accurate quantum mechanical (QM) method to study condensed-phase and enzymatic chemical reactions via mixed QM and molecular mechanical (QM/MM) simulations. As an initial test, the Menshutkin reaction between NH(3) and CH(3) Cl in water was computed using a RM1/TIP4P-Ew/CM3R procedure and the resultant ΔG(‡) , ΔG(rxn) , and geometries were in reasonable accord with other computational methods; however, some potentially serious shortcomings in RM1 are discussed.

Dielectric Properties of N,N-Dimethylformamide Aqueous Solutions in External Electromagnetic Fields by Molecular Dynamics Simulation

Nonequilibrium molecular dynamics (NMD) simulations of the N, N-dimethylformamide (DMF) aqueous solution have been performed in the canonical ensemble (NVT) in both the absence and presence of external electromagnetic (E/M) field, using the SPC/E model for water and the optimized potentials for liquid simulations-all atom (OPLS-AA) model for DMF. The electromagnetic wave propagates in the z-axis direction with a frequency of 10 GHz, and the intensity of the electromagnetic field in the range 0 to 3 x 10(9) V/m is assumed in the simulation. The results indicate that as the intensity of the electromagnetic field increased, the dipole alignment of the DMF aqueous solution molecules became more pronounced and the molecular polarizability gradually increased. In addition, the hydration number and the static dielectric constant of DMF aqueous solutions decreased as the intensity of the electromagnetic field increased.

In silico prediction of drug solubility: 4. Will simple potentials suffice?

In view of the extreme importance of reliable computational prediction of aqueous drug solubility, we have established a Monte Carlo simulation procedure which appears, in principle, to yield reliable solubilities even for complex drug molecules. A theory based on judicious application of linear response and mean field approximations has been found to reproduce the computationally demanding free energy determinations by simulation while at the same time offering mechanistic insight. The focus here is on the suitability of the model of both drug and solvent, i.e., the force fields. The optimized potentials for liquid simulations all atom (OPLS-AA) force field, either intact or combined with partial charges determined either by semiempirical AM1/CM1A calculations or taken from the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field has been used. The results illustrate the crucial role of the force field in determining drug solubilities. The errors in interaction energies obtained by the simple force fields tested here are still found to be too large for our purpose but if a component of this error is systematic and readily removed by empirical adjustment the results are significantly improved. In fact, consistent use of the OPLS-AA Lennard-Jones force field parameters with partial charges from the COMPASS force field will in this way produce good predictions of amorphous drug solubility within 1 day on a standard desktop PC. This is shown here by the results of extensive new simulations for a total of 47 drug molecules which were also improved by increasing the water box in the hydration simulations from 500 to 2000 water molecules.

Molecular Dynamics Simulation for Formamide Aqueous Solution

In order to know more about the microcosmic structure of the important biochemical model molecule formamide (FM) in aqueous solution, the Optimized Potentials for Liquid Simulations-All Atom (OPLSAA) model were used in the molecular dynamics (MD) simulation for the aqueous solution of FM in the whole concentration range. The radial distribution functions of the solutions were obtained. The interaction between water molecule and FM molecule was analyzed and calculated. It was found that there was a weak interaction (C-H...O) between the C-H beside the carbonyl of FM and water. The weak interaction could not be ignored, which was suggested to be significant in preventing the tautomerization of FM, especially when the concentration of FM increased in the aqueous solution of FM. By doing the calculation in the whole concentration range of the aqueous solution of FM, it was found that FM could strengthen the local structure of water in water-rich region. As the concentration increased, the association of water itself would be replaced by cross-association between water and FM gradually. In the FM-rich region, it was mainly the linear association of FM itself.