OPLS-AA Force Field Research Articles

Critical Polyalkane, Polyether, and Polysilicone Structure Differences: Consideration of Polymer Forces from the OPLS-AA Standpoint

The OPLS-AA force field is well established in determining the bulk properties of molecules from molecular parameterizations. However, the comparison of such derived properties from high performance computing research has not extended to determine their applicability or breakdown in polyalkane, polyether and polysilicone materials, specifically in the context of surface activity. This letter highlights the differences in these structures attractive and repulsive forces while detailing the distances between charge centers. This paper describes the types of interactions within the OPLS-AA force field that explain polyether and polysilicone material solvophilicity, with particular focus on mixed solvent systems. It details how the solvophilicity varies with the relative strength of interactions for these materials at various alcohol contents.

Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals.

First principles prediction of the structure, thermodynamics and solubility of organic molecular crystals, which play a central role in chemical, material, pharmaceutical and engineering sciences, challenges both potential energy functions and sampling methodologies. Here we calculate absolute crystal deposition thermodynamics using a novel dual force field approach whose goal is to maintain the accuracy of advanced multipole force fields (e.g. the polarizable AMOEBA model) while performing more than 95% of the sampling in an inexpensive fixed charge (FC) force field (e.g. OPLS-AA). Absolute crystal sublimation/deposition phase transition free energies were determined using an alchemical path that grows the crystalline state from a vapor reference state based on sampling with the OPLS-AA force field, followed by dual force field thermodynamic corrections to change between FC and AMOEBA resolutions at both end states (we denote the three step path as AMOEBA/FC). Importantly, whereas the phase transition requires on the order of 200 ns of sampling per compound, only 5 ns of sampling was needed for the dual force field thermodynamic corrections to reach a mean statistical uncertainty of 0.05 kcal mol-1. For five organic compounds, the mean unsigned error between direct use of AMOEBA and the AMOEBA/FC dual force field path was only 0.2 kcal mol-1 and not statistically significant. Compared to experimental deposition thermodynamics, the mean unsigned error for AMOEBA/FC (1.4 kcal mol-1) was more than a factor of two smaller than uncorrected OPLS-AA (3.2 kcal mol-1). Overall, the dual force field thermodynamic corrections reduced condensed phase sampling in the expensive force field by a factor of 40, and may prove useful for protein stability or binding thermodynamics in the future.

Low Hanging Fruit in Computational Molecular Dynamics Simulations with the Published OPLS-AA Force Field

After performing computations in molecular dynamics in high performance research systems, many solvable but yet unsolved problems have been determined. These include (i) a list of molecules which are of commercial and scholarly interest that can be parameterized with the available OPLS-AA literature, (ii) a list of metals in certain environments which have yet to be parameterized and would provide insight into their behavior in commercial processes, (iii) an empirical approach to searching for the impact of molecular parameterizations on observable properties which is useful in searching for new materials, and (iv) understanding molecular reactivity in computational molecular dynamics.

Counting the Relative Number of Hydrogen Bonds in Several Alcohol Co-solvated Systems via GROMACS

In order to better understand the solubility properties of polyalkane, polyether and polysilicone materials, which are critical to the foaming behavior of shampoo and shaving creams, GROMACS molecular dynamics NVT simulations were performed using the OPLS-AA force field to determine the time-average number of hydrogen bonds in solutions of water co-solvated with methanol, ethanol, isopropanol, dimethyl ketone and acetyl methyl carbinol.

Extension of the LOPLS-AA Force Field for Alcohols, Esters, and Monoolein Bilayers and its Validation by Neutron Scattering Experiments.

The recently presented LOPLS-AA all-atom force field for long hydrocarbon chains, based on the OPLS-AA force field, was extended to alcohols, esters, and glyceryl monooleate (GMO) lipids as a model lipid. Dihedral angles were fitted against high level ab initio calculations, and ester charges were increased to improve their hydration properties. Additionally, the ester Lennard-Jones parameters were readjusted to reproduce experimental liquid bulk properties, densities, and heats of vaporization. This extension enabled the setup of LOPLS-AA parameters for GMO molecules. The properties of the lipid force field were tested for the liquid-crystalline phase of a GMO bilayer. The obtained area per lipid for GMO is in good agreement with experiment. Additionally, the lipid dynamics on the subpicosecond to the nanosecond time scale is in excellent agreement with results from time-of-flight (TOF) quasielastic neutron scattering (QENS) experiments on a multilamellar monoolein system, enabling here for the first time the critical evaluation of the short-time dynamics obtained from a molecular dynamics simulation of a membrane system.

The surface activity of polymers in cosolvated systems determined from computational simulation

The present body of literature fails to adequately address the need for simulation metrics which determine the surface activity of target species in single or multi-solvent systems. Within this work a new property determinable by computational molecular dynamics simulation is detailed. That is the surface parameter, which is an indicator of the placement of a molecule with respect to the interface. Simulations were carried out on polyalkanes in alcohol co-solvated systems to verify systematically that the OPLS-AA force fields can accurately describe the solvation of low molecular weight polyalkanes with increased alcohol content. This parameter and the associated code are helpful in identifying quickly if a molecule is surface active, especially in mixed solvent systems. The code for the determination of this property is written in FORTRAN, a widespread and readily available package on most supercomputing systems where GROMACS is deployed.

Force-Field Based Quasi-Chemical Method for Rapid Evaluation of Binary Phase Diagrams.

We present the Pair Configurations to Molecular Activity Coefficients (PAC-MAC) method. The method is based on the pair sampling technique of Blanco (Fan, C. F.; Olafson, B. D.; Blanco, M.; Hsu, S. L. Application of Molecular Simulation to Derive Phase Diagrams of Binary Mixtures. Macromolecules 1992, 25, 3667-3676) with an extension that takes the packing of the molecules into account by a free energy model. The intermolecular energy is calculated using classical force fields. PAC-MAC is able to predict activity coefficients and corresponding vapor-liquid equilibrium diagrams at least 4 orders of magnitude faster than molecular simulations. The accuracy of the PAC-MAC method is tested by comparing the results with experimental data and with the results of the COSMO-SAC model (Lin, S.-T.; Sandler, S. I. A Priori Phase Equilibrium Prediction from a Segment Contribution Solvation Model. Ind. Eng. Chem. Res. 2002, 41, 899-913). PAC-MAC (using the OPLS-aa force field) is shown to be comparable in accuracy to COSMO-SAC, at the considerable advantage that PAC-MAC in principle does not require quantum calculation, provided proper force fields to be available.

Topologies, structures and parameter files for lipid simulations in GROMACS with the OPLS-aa force field: DPPC, POPC, DOPC, PEPC, and cholesterol.

In this data article we provide topologies and force field parameters files for molecular dynamics simulations of lipids in the OPLS-aa force field using the GROMACS package. This is the first systematic parameterization of lipid molecules in this force field. Topologies are provided for four phosphatidylcholines: saturated DPPC, mono-cis unsaturated POPC and DOPC, and mono-trans unsaturated PEPC. Parameterization of the phosphatidylcholines was achieved in two steps: first, we supplemented the OPLS force field parameters for DPPC with new parameters for torsion angles and van der Waals parameters for the carbon and hydrogen atoms in the acyl chains, as well as new partial atomic charges and parameters for torsion angles in the phosphatidylcholine and glycerol moieties [1]. Next, we derived parameters for the cis and trans double bonds and the neighboring them single bonds [2]. Additionally, we provide GROMACS input files with parameters describing simulation conditions (md.mdp), which are strongly recommended to be used with these lipids models. The data are associated with the research article “Cis and trans unsaturated phosphatidylcholine bilayers: a molecular dynamics simulation study” [2] and provided as supporting materials.

A computer model of a polyunsaturated monogalactolipid bilayer.

1,2-di-O-acyl-3-O-β-D-galactopyranosyl-sn-glycerol (MGDG) is the main lipid component of thylakoid membranes of higher plants and algae. This monogalactolipid is thought of as a non-bilayer lipid but actually it can form both lamellar and nonlamellar phases. In this study, molecular dynamics (MD) simulations of the fully hydrated di-18:3 MGDG bilayer in the lamellar phase were carried out at 310 and 295 K for 200 and 450 ns, respectively, using the GROMACS 4 software package and OPLS-AA force field. At both temperatures, the lamellar phase of the systems was stable. The pure di-18:3 MGDG bilayer is the first step towards creating a computer model of the lipid matrix of the thylakoid membrane and the main aim of this study was to validate the computer model of di-18:3 MGDG in the bilayer and also to assess the properties of the bilayer. However, only a few of the predicted properties could be compared with those derived experimentally and in other MD simulations because of insufficient amount of such data. Thus, direct validation of the MGDG bilayer proved difficult. Therefore, in the validation process also an indirect approach was used, in which a computer model of the 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) bilayer simulated at the same temperatures using the same force field as the MGDG bilayer was assessed. Successful validation of the DOPC bilayer parameterized in the OPLS-AA force field and similar properties of the MGDG molecules in the pure 18:3 MGDG and in binary 18:3 MGDG-PC bilayers indicate that the computer model of the MDGD molecule is faithful and the MGDG bilayer is representative on the time scales covered in these MD simulations.

Evaluation of CM5 Charges for Nonaqueous Condensed-Phase Modeling.

Partial atomic charges for neutral molecules from quantum mechanical calculations are typically scaled for use in molecular modeling of liquid-phase systems. Optimal scale factors of 1.14 for CM1A and 1.27 for CM5 charges were previously determined for minimizing errors in free energies of hydration. The adequacy of the 1.14*CM1A and 1.27*CM5 models are evaluated here in pure liquid simulations in combination with the OPLS-AA force field. For 22 organic liquids, the 1.14*CM1A and 1.27*CM5 models yield mean unsigned errors (MUEs) of ca. 1.40 kcal/mol for heats of vaporization. Not surprisingly, this reflects overpolarization with the scale factors derived for aqueous media. Prediction of pure liquid properties using CM5 charges is optimized using a scale factor of 1.14, which reduces the MUE for heats of vaporization to 0.89 kcal/mol. However, due to the impracticality of using different scale factors in different explicit-solvent condensed-phase simulations, a universal scale factor of 1.20 emerged for CM5 charges. This provides a balance between errors in computed pure liquid properties and free energies of hydration. Computation of free energies of hydration by the GB/SA method further found that 1.20 is equally suited for use in explicit or implicit treatments of aqueous solvation. With 1.20*CM5 charges, a variety of condensed-phase simulations can be pursued while maintaining average errors of 1.0 kcal/mol in key thermodynamic properties.

AIMD Results for a Concentrated Solution of Tetra-ethylammonium Tetra-fluoroborate in Propylene Carbonate

Ab initio molecular dynamics (AIMD) calculations are implemented for a concentrated solution of tetra-ethylammonium tetra-fluoroborate in propylene carbonate (TEABF4/PC), which is of interest in electrochemical double-layer capacitors. AIMD calculations predict more sharply structured ion-ion center partial radial distributions than either GAFF or OPLS-aa force-fields in classic FFMD calculations. This may be due to AIMD refinement of van der Waals interactions which drive ion-pairing and phase separation of TEABF4 from PC at this elevated concentration. Quantifying the charge transfer of BF4 - and N(CH2CH3)4 + ions to neighboring solution species, the (Bader) partial charges of BF4 - and N(CH2CH3)4 + ions in PC solution differ from the formal charges by being smaller in magnitude by about 5%.

Dielectric Properties of Ethylene Carbonate and Propylene Carbonate Using Molecular Dynamics Simulations

Ethylene carbonate (EC) and propylene carbonate (PC) are two widely used solvents in Li-ion batteries and supercapacitors. Ion diffusion in these solvents depends strongly on accurate predictions of solvent dielectric properties. We used all-atom molecular dynamics simulations of these pure solvents to calculate dielectric constants and dielectric relaxation times at various temperatures. The dielectric constant measures polarization of a material whereas dielectric relaxation measures the lag of the polarization in a dielectric medium in responding to a change in an applied field. Predicted values are compared with the available experimental results to validate the force field parameters (OPLS-AA) for these solvents. Current results for dielectric constant and dielectric relaxation time indicate that OPLS-AA force field produces reasonable agreement with experiment for both EC and PC. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U. S. Department of Energys National Nuclear Security Administration under contract DE-AC04-94AL85000

Improved Peptide and Protein Torsional Energetics with the OPLSAA Force Field.

The development and validation of new peptide dihedral parameters are reported for the OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ1, and χ2 potential energy surfaces for blocked dipeptides. New Fourier coefficients for the dihedral angle terms of the OPLS-AA force field were fit to these surfaces, utilizing a Boltzmann-weighted error function and systematically examining the effects of weighting temperature. To prevent overfitting to the available data, a minimal number of new residue-specific and peptide-specific torsion terms were developed. Extensive experimental solution-phase and quantum chemical gas-phase benchmarks were used to assess the quality of the new parameters, named OPLS-AA/M, demonstrating significant improvement over previous OPLS-AA force fields. A Boltzmann weighting temperature of 2000 K was determined to be optimal for fitting the new Fourier coefficients for dihedral angle parameters. Conclusions are drawn from the results for best practices for developing new torsion parameters for protein force fields.

Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field.

Adenylate kinase is a widely used test case for many conformational transition studies. It performs a large conformational transition between closed and open conformations while performing its catalytic function. To understand conformational transition mechanism and impact of force field choice on E. Coli adenylate kinase, we performed all-atom explicit solvent classical molecular dynamics simulations starting from the closed conformation with four commonly used force fields, namely, Amber99, Charmm27, Gromos53a6, Opls-aa. We carried out 40 simulations, each one 200ns. We analyzed completely 12 of them that show full conformational transition from the closed state to the open one. Our study shows that different force fields can have a bias toward different transition pathways. Transition time scales, frequency of conformational transitions, order of domain motions and free energy landscapes of each force field may also vary. In general, Amber99 and Charmm27 behave similarly while Gromos53a6 results have a resemblance to the Opls-aa force field results.

Role of side-chain interactions on the formation of α-helices in model peptides.

The role played by side-chain interactions on the formation of α-helices is studied using extensive all-atom molecular dynamics simulations of polyalanine-like peptides in explicit TIP4P water. The peptide is described by the OPLS-AA force field except for the Lennard-Jones interaction between Cβ-Cβ atoms, which is modified systematically. We identify values of the Lennard-Jones parameter that promote α-helix formation. To rationalize these results, potentials of mean force (PMF) between methane-like molecules that mimic side chains in our polyalanine-like peptides are computed. These PMF exhibit a complex distance dependence where global and local minima are separated by an energy barrier. We show that α-helix propensity correlates with values of these PMF at distances corresponding to Cβ-Cβ of i-i+3 and other nearest neighbors in the α-helix. In particular, the set of Lennard-Jones parameters that promote α-helices is characterized by PMF that exhibit a global minimum at distances corresponding to i-i+3 neighbors in α-helices. Implications of these results are discussed.

Evaluation of the OPLS-AA force field for the study of structural and energetic aspects of molecular organic crystals.

Motivated by the need for reliable experimental data for the assessment of theoretical predictions, this work proposes a data set of enthalpies of sublimation determined for specific crystalline structures, for the validation of molecular force fields (FF). The selected data were used to explore the ability of the OPLS-AA parametrization to investigate the properties of solid materials in molecular dynamics simulations. Furthermore, several approaches to improve this parametrization were also considered. These modifications consisted in replacing the original FF atomic point charges (APC), by values calculated using quantum chemical methods, and by the implementation of a polarizable FF. The obtained results indicated that, in general, the best agreement between theoretical and experimental data is found when the OPLS-AA force field is used with the original APC or when these are replaced by ChelpG charges, computed at the MP2/aug-cc-pVDZ level of theory, for isolated molecules in the gaseous phase. If a good description of the energetic relations between the polymorphs of a compound is required then either the use of polarizable FF or the use of charges determined taking into account the vicinity of the molecules in the crystal (combining the ChelpG and MP2/cc-pVDZ methods) is recommended. Finally, it was concluded that density functional theory methods, like B3LYP or B3PW91, are not advisable for the evaluation of APC of organic compounds for molecular dynamic simulations. Instead, the MP2 method should be considered.

Effect of partial atomic charges on the calculated free energy of solvation of poly(vinyl alcohol) in selected solvents.

It is well-known that properties of poly(vinyl alcohol) (PVA) in the pure and solution states depend largely on the hydrogen bonding networks formed. In the context of molecular simulation, such networks are handled through the Coulombic interactions. Therefore, a good set of partial atom charges (PACs) for simulations involving PVA is highly desirable. In this work, we calculated the PACs for PVA using a few commonly used population analysis schemes with a hope to identify an accurate set of PACs for PVA monomers. To evaluate the quality of the calculated parameters, we have benchmarked their predictions for free energy of solvation (FES) in selected solvents by molecular dynamics simulations against the ab initio calculated values. Selected solvents were water, ethanol and benzene as they covered a range of size and polarity. Also, PVA with different tacticities were used to capture their effect on the calculated FESs. Based on our results, neither PACs nor FESs are affected by the chain tacticity. While PACs predicted by the Merz-Singh-Kollman scheme were close to original values in the OPLS-AA force field in way that no significant difference in properties of pure PVA was observed, free energy of solvation calculated using such PACs showed greater agreement with ab initio calculated values than those calculated by OPLS-AA (and all other schemes used in this work) in all three solvents considered.

Relationship between unbranched alkane dimer interaction energies using different theoretical methods and correlations with thermodynamic properties

Interaction energies (Eint) were evaluated for n-alkanes dimers (C1–C10) using DFT-D, different functionals, and several basis sets. In addition, calculations were also carried out with DFTB-LD and MM3 and OPLS-AA force fields. Results show linear correlations of Eint with respect to those obtained from literature at high levels of theory (MP2 and CCSD(T)). Relationships between Eint and experimental heats of vaporization (ΔHv) and critical temperatures (Tc) were obtained with MP2, DFT-D, MM and DFTB-LD. This leads to good extrapolations for hairpin-hexadecane using MM3 and DFTB-LD for ΔHv and Tc, respectively. Dispersion in DFT is discussed.

36. Conformational flexibility of cyclic imine phycotoxins revealed by long-timescale molecular dynamics simulations

Macrocyclic spiroimine phycotoxins constitute a growing class of structurally related marine neurotoxins contaminating shellfish (Molgo et al., 2014). Most of them are strong antagonists of nicotinic acetylcholine receptors (nAChRs), and a few ones showed moderate activities against muscarinic acetylcholine receptors (mAChRs). During recent years this field has witnessed important developments with regard to chemical synthesis, X-ray crystallography, electrophysiology, detection methods and molecular modelling. In this study, the conformational flexibility of representative cyclic imine phycotoxins (gymnodimines, spirolides, pinnatoxins, pteriatoxins, spiro-prorocentrimine and prorocentrolides) was evaluated using long-timescale all-atom molecular dynamics simulations in OPLS-AA force field.

Molecular dynamics simulations of complex mixtures aimed at the preparation of naproxen-imprinted xerogels.

The main objective of this study was to simulate for the first time a complex sol-gel system aimed at preparing the (S)-naproxen-imprinted xerogel with an explicit representation of all the ionic species at pH 9. For this purpose, a series of molecular dynamics (MD) simulations of different mixtures, including species never studied before using the OPLS-AA force field, were prepared. A new parametrization for these species was developed and found to be acceptable. Three different systems were simulated, representing two types of pregelification models: the first one represented the initial mixture after complete hydrolysis and condensation to cyclic trimers (model A); the second one corresponded to the same mixture after the evaporation process (model B); and the last one was a simpler initial mixture without an explicit representation of all of the imprinting-mixture constituents (model C). The comparison of systems A and C mainly served the purpose of evaluating whether an explicit representation of all of the components (model A) was needed or if a less computationally demanding system in which the alkaline forms of the silicate species were ignored (model C) would be sufficient. The results confirmed our hypothesis that an explicit representation of all of the imprinting-mixture constituents is essential to study the molecular imprinting process because a poor representation of the ionic species present in the mixture may lead to erroneous conclusions or lost information. In general, the radial distribution function (RDF) analysis and interaction energies demonstrated a high affinity of the template molecule, 2-(6-methoxynaphthalen-2-yl)propanoate (NAP(-), the conjugate base of (S)-naproxen), for the gel backbone, especially targeting the units containing the dihydroimidazolium moiety used as a functional group. Model B, representing a nearly gelled sol where the density of silicates and solvent polarity were much higher relative to the other models, allowed for much faster simulations. That gave us the chance to observe the templating effect through a comparative analysis and observation of the trajectories from simulations with the template- versus non-template-containing mixtures. Overall, a strong coherence between the imprinting-relevant interactions, aggregation, or the silicate network texturing effects taken out of the simulations and the experimentally high imprinting performance and porosity features of the corresponding gels was achieved.