COMPASS Force Field Research Articles

Molecular Dynamics Simulation of Mahkota Dewa (Phaleria Macrocarpa) Extract in Subcritical Water Extraction Process

Mahkota Dewa (Phaleria Macrocarpa), a good source of saponin, flavanoid, polyphenol, alkaloid, and mangiferin has an extensive range of medicinal effects. The intermolecular interactions between solute and solvents such as hydrogen bonding considered as an important factor that affect the extraction of bioactive compounds. In this work, molecular dynamics simulation was performed to elucidate the hydrogen bonding exists between Mahkota Dewa extracts and water during subcritical extraction process. A bioactive compound in the Mahkota Dewa extract, namely mangiferin was selected as a model compound. The simulation was performed at 373 K and 4.0 MPa using COMPASS force field and Ewald summation method available in Material Studio 7.0 simulation package. The radial distribution functions (RDF) between mangiferin and water signify the presence of hydrogen bonding in the extraction process. The simulation of the binary mixture of mangiferin:water shows that strong hydrogen bonding was formed. It is suggested that, the intermolecular interaction between OH2O••HMR4(OH1) has been identified to be responsible for the mangiferin extraction process.

Molecular dynamics simulation for studying the stability of structure H clathrate-hydrates of argon and large guest molecules

ABSTRACTThe aim of present paper is to study the stability of (argon + large guest molecules) structure H clathrate-hydrates by using molecular dynamics simulations and with employing the COMPASS force field to consider the molecular interactions. The simulations are performed by embedding the structure H clathrate-hydrates in a simulation cell under isobaric-isothermal (NPT) conditions. The obtained equilibrium lattice parameters are compared with the experimental data, where a good consistency is observed. The results show that the size and dipole moment of the guest molecules enclosed in the hydrate cages play the main role in the interactions between the guest molecules and the water molecules, which constitute the surrounding walls of the hydrate cage and these interactions would stabilize the hydrate structure. The characteristics of the clathrate-hydrate structure are analyzed by evaluating the radial distribution function, where the agreement between the results obtained in this work and other similar theoretical and experimental investigations validates the simulation procedure and related interpretations.

Comparative studies on structure, sensitivity and mechanical properties of CL-20/DNDAP cocrystal and composite by molecular dynamics simulation.

Molecular dynamics simulation was performed on 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20), 2,4-dinitro-2,4-diazapentane (DNDAP), and CL-20/DNDAP cocrystal and composite under COMPASS force field at different temperatures. The binding energy (Ebind), radial distribution function (RDF), trigger bond length, cohesive energy density (CED) and mechanical properties were studied and compared. The results show that the binding energy of the cocrystal is evidently higher than that of the composite at the same temperature. RDF analysis reveals that hydrogen bonds and vdW forces between CL-20 and DNDAP exist in both CL-20/DNDAP cocrystal and composite, and the interactions in the cocrystal are stronger than those in the composite. The maximum trigger bond length decreases in the order ε-CL-20 > CL-20/DNDAP composite > CL-20/DNDAP cocrystal. Moreover, the rigidity and stiffness of the cocrystal and composite decrease compared to that of CL-20, while the ductility and elasticity are better than that of the two pure components. These results demonstrate that CL-20/DNDAP cocrystal might be very promising in explosive applications.

Molecular dynamics simulations on ε-CL-20-based PBXs with added GAP and its derivative polymers.

Molecular dynamics simulations have been employed to study the ε-CL-20-based PBXs under COMPASS force field. ε-CL-20 was chosen as the base explosive due to its higher energy, density and detonation performance than conventional explosives. Four polymers, GAP, GAP-NH2, GAP-NO2 and GAP-NH2-NO2 were added into the ε-CL-20(001) crystalline surface to build the PBX models. The cohesive energy densities (CEDs), elastic coefficients, isotropic mechanical properties (Young's moduli, bulk moduli, shear moduli, Poisson's ratio, Cauchy pressure and K/G) and initiation bond length distribution were studied. It turned out that the CEDs order was A1 < A4 < A3 < A2 < A. The mechanical properties of pure ε-CL-20(001) were effectively improved by building PBX models. System A3 showed better comprehensive mechanical properties than the other three PBXs. A study on the initiation bond length distribution showed that the Lmax and Lave of N–NO2 increased with increasing temperature and they were related to the sensitivity of the explosives. The order of Lmax was A3 < A4 < A2 < A1 < A, which indicated that the PBXs owned lower sensitivity than system A. These studies are thought to provide guidance for further research on the application of GAP and its derivative polymers. Meanwhile, they are meaningful for the studies on ε-CL-20-based PBXs.

Molecular Dynamic Simulation and Density Functional Theory Insight into the Nitrogen Rich explosive 1,5-diaminotetrazole(DAT)

Abstract 1,5-diaminotetrazole is of much interest to researchers because of the nitrogen-rich and insensitive properties. Molecular dynamic and density functional theory were used to study the properties of 1,5-diaminotetrazole. Molecular dynamic (MD) simulation was conducted for 1,5-diaminotetrazole using COMPASS force field with NVT ensemble. The results show that the lattice parameters changed a little before 500k, while rise suddenly at 503k indicating the phase transition taking place. The density functional theory study shows the change of density of states at higher pressure. The band gaps decrease with the increase of pressures. In the region of 0-45GPa, the band gaps decrease suddenly. Band gap changes a little in the region of 45-55GPa, showing the crystal structure is harf to be compressed. Hirshfeld surfaces were employed to analysis the intermolecular interactions in 1,5-diaminotetrazole, and the results show that H…N hydrogen bond was the dominant weak interaction. The calculations of dominant crystal facets of DAT showing that DAT possesses five dominant crystal facets: (100), (011), (002), (10-2) and (110).

Краевые колебания нанолент графана

AbstractUsing the COMPASS force field, natural linear vibrations of graphane (graphene hydrogenated on both sides) nanoribbons are simulated. The frequency spectrum of a graphane sheet consists of three continuous intervals (low-frequency, mid-frequency, and narrow high-frequency) and two gaps between them. The construction of dispersion curves for nanoribbons with a zigzag and chair structure of the edges show that the frequencies of edge vibrations (edge phonons) can be present in the gaps of the frequency spectrum. In the first type of nanoribbons, two dispersion curves are in the low-frequency gap of the spectrum and four dispersion curves in the second gap. These curves correspond to phonons moving only along the nanoribbon edges (the mean depth of their penetration toward the nanoribbon center does not exceed 0.15 nm).

Molecular mechanics and dynamics simulation of hydrogen diffusion in aluminum melt

The main impurities in aluminum melt are hydrogen and Al2O3, which can deteriorate melt quality and materials performance. However, the diffusion process of H atoms in aluminum melt and the interactions among Al atoms, Al2O3 and hydrogen have been studied rarely. Molecular mechanics and dynamics simulations are employed to study the diffusion behaviors of different types of hydrogen, such as free H atoms, H atoms in H2 and H+ ions in H2O using COMPASS force field. Correspondingly, force field types h, h1h and h1o are used to describe different types of hydrogen which are labeled as Hh, Hh1h and Hh1o. The results show that the adsorption areas are maximum for Hh1o, followed by Hh1h and Hh. The diffusion ability of Hh1o is the strongest whereas Hh is hard to diffuse in aluminum melt because of the differences in radius and potential well depth of various types of hydrogen. Al2O3 cluster makes the Al atoms array disordered, creating the energy conditions for hydrogen diffusion in aluminum melt. Al2O3 improves the diffusion of Hh and Hh1o, and constrains Hh1h which accumulates around it and forms gas porosities in aluminum. Hh1o is the most dispersive in aluminum melt, moreover, the distance of Al-Hh1o is shorter than that of Al-Hh1h, both of which are detrimental to the removal of Hh1o. The simulation results indicate that the gas porosities can be eliminated by the removal of Al2O3 inclusions, and the dispersive hydrogen can be removed by adsorption function of gas bubbles or molten fluxes.

Comparative studies on structures, mechanical properties, sensitivity, stabilities and detonation performance of CL-20/TNT cocrystal and composite explosives by molecular dynamics simulation.

To investigate and compare the differences of structures and properties of CL-20/TNT cocrystal and composite explosives, the CL-20/TNT cocrystal and composite models were established. Molecular dynamics simulations were performed to investigate the structures, mechanical properties, sensitivity, stabilities and detonation performance of cocrystal and composite models with COMPASS force field in NPT ensemble. The lattice parameters, mechanical properties, binding energies, interaction energy of trigger bond, cohesive energy density and detonation parameters were determined and compared. The results show that, compared with pure CL-20, the rigidity and stiffness of cocrystal and composite models decreased, while plastic properties and ductility increased, so mechanical properties can be effectively improved by adding TNT into CL-20 and the cocrystal model has better mechanical properties. The interaction energy of the trigger bond and the cohesive energy density is in the order of CL-20/TNT cocrystal > CL-20/TNT composite > pure CL-20, i.e., cocrystal model is less sensitive than CL-20 and the composite model, and has the best safety parameters. Binding energies show that the cocrystal model has higher intermolecular interaction energy values than the composite model, thus illustrating the better stability of the cocrystal model. Detonation parameters vary as CL-20>cocrystal > composite, namely, the energy density and power of cocrystal and composite model are weakened; however, the CL-20/TNT cocrystal explosive still has desirable energy density and detonation performance. This results presented in this paper help offer some helpful guidance to better understand the mechanism of CL-20/TNT cocrystal explosives and provide some theoretical assistance for cocrystal explosive design.

Synthesis, molecular dynamic simulation, and density functional theory insight into the cocrystal explosive of 2,4,6-trinitrotoluene/1,3,5-trinitrobenzene

This paper reports the experimental and theoretical studies of the synthesis and behavior of a cocrystal energetic material 2,4,6-trinitrotoluene/1,3,5-trinitrobenzene (TNT/TNB). The performance tests show that this material is more powerful and less sensitive than TNT and TNB. A molecular dynamic simulation is conducted for the cocrystal TNT/TNB by using a COMPASS force field with an NPT ensemble. The density function theory is applied to investigate the band structure and the density of states for various pressures and temperatures. The results show that the TNT/TNB crystal is sensitive to pressures in the interval of 35–50 GPa, and the melting temperature of the crystal is around ≈320 K, which agrees well with experimental results. The Hirshfeld analysis is carried out to ascertain weak interactions and associated two-dimensional fingerprint plots. The crystal packing is demonstrated to be ensured by H· · · O, C· · · O, and O· · ·O contacts.

Theoretical simulations on the glass transition temperatures and mechanical properties of modified glycidyl azide polymer

Molecular dynamics (MD) simulations were carried out to study the glass transition temperature and mechanical properties of glycidyl azide polymer (GAP) most widely used in propellants and explosives as an energetic binder. Other three polymers derived from GAP with different side groups were designed and simulated under the COMPASS force field, with the ensembles of constant particle number, volume, temperature (NVT) and constant particle number, pressure, temperature (NPT). It was found that the densities and free volumes of polymers changed regularly along with the decrease of temperature and the transition occurred at the turning point. Thus the glass transition temperatures (Tg) were predicted in two methods based on density and free volume theory. The simulation results showed that the introduction of –NO2 made important contribution on reducing the Tg of polymers, and the probable mechanism was discussed. Moreover, several mechanical properties of four pure polymer systems such as Young’s modulus, Shear modulus, Bulk modulus and Poisson’s ratio, etc, were calculated. The calculated results revealed that the single introduction of –NO2 increased the mechanical properties parameters more obviously than other two polymers. Overall, a new method was used for GAP modification in order to improve its mechanical properties at low temperatures, and provides some guidance to the GAP modification via changing substituent groups of side chain.

INVESTIGATING THE ROLE OF MOLECULAR INTERACTIONS IN POLYMORPHISM OF MEFENAMIC ACID IN ETHYL ACETATE SOLUTION

Mefenamic acid, a widely used nonsteroidal anti-inflammatory and analgesic agent, is one of the active pharmaceutical ingredients that exhibit polymorphisms. This study reports a combined experimental and molecular dynamics simulation study of mefenamic acid crystallization in ethyl acetate. The solid-state characterization of the polymorph produced using Fourier transform infrared spectroscopy (FTIR), X-Ray powder diffractometer (XPRD), and differential scanning calorimetry (DSC) analysis show the characteristic of Form I, which were N-H stretching at 3313cm-1, two endothermic peaks, and significant XPRD peaks at 6.3°, 13.8°, 15.9°, 21.3°, and 26.3°. The molecular dynamics simulations were performed using COMPASS force field available in the Material Studio 5.5 simulation package. The simulations were run for equilibration with a time step of 1 fs for a period of 250 ps and 2000 ps simulation in NVE (constant number of atoms, volume and energy) and NPT (constant number of atoms, pressure and temperature) thermodynamic ensemble, respectively. The trajectory files from the simulation were analyzed for radial distribution function (RDF) to investigate the intermolecular interactions. The simulation results showed strong solute-solute and solute-solvent interactions, which were O1MA•••H15MA and O1EA•••H15MA. These findings revealed the presence of hydrogen bonds that contributes to the solvation and formation of hydrogen motif in polymorphic Form I of mefenamic acid during crystallization with ethyl acetate as a solvent.

Adsorption of dihalogen molecules on pristine graphene surface: Monte Carlo and molecular dynamics simulation studies.

Weak interactions of graphene surface with reactive molecular impurities are the subject of many studies since noncovalent functionalization of surface via molecular doping is a powerful tool for tuning the electronic properties of graphene layers. In this work, the adsorption of diatomic halogen gas molecules, F2, Cl2, Br2, I2 onto bilayer and multilayer pristine graphene surfaces were studied comparatively by Monte Carlo (MC) and molecular dynamics (MD) simulation techniques in canonical ensemble. The adsorption sites, adsorption capacity, coverage factors, adsorption isotherms, and adsorption kinetics were investigated and the adsorption energies were calculated for all adsorbates. Graphene was modeled as a two-dimensional layer of 200 carbon atoms in a honeycomb arrangement. The COMPASS force field was used in the simulations. The adsorption isotherms were obtained and fitted to Langmuir model. The kinetics of adsorption was studied and found to be first order. Both the monolayer and the multilayer adsorption of halogen molecules showed that van der Waals volumes of halogen molecules and also their polarizabilities display a competitive role in the saturation capacity and the strength of surface interactions.

Synthesis and characterization of Torlon-based polyion complex for direct methanol and polymer electrolyte membrane fuel cells

An acid–base polyion complex membrane was synthesized by blending a polyamide-imide (Torlon) with sulfonated polyethersulfone (SPES), to make a sturdy proton-conducting electrolyte for portable fuel cells. The membrane was characterized by FTIR, XRD, TGA, SEM and UTM techniques. Chemical interactions between Torlon and SPES enabled the formation of ionic clusters that are useful for facilitating proton conduction and water sorption with prevention of fuel bypass. The complex exhibited high mechanical, thermal and oxidative stability with low methanol permeability (9.46 × 10−8 cm2/s). Sorption experiments showed the membrane to possess moderate affinity toward water with preferably low methanol uptake. Moreover, the blend membrane exhibited high proton conductivity (0.13 S/cm) at low humidity and high temperature conditions. To investigate the microstructure and transport behavior of the reported blend, molecular dynamics simulation based on COMPASS force field was performed. The diffusivity of hydronium ion obtained through simulation was used to calculate conductivity by Einstein equation. Proton conductivity obtained by simulation was validated by comparison with experimental data. Furthermore, the interaction of membrane functional groups with water and hydronium ion carrier was evaluated by radial distribution function. The study revealed the proposed complex to be an attractive, inexpensive alternative to state-of-the-art Nafion 117 membrane for fuel cell application.

The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine.

Motional averaging has been proven to be significant in predicting the chemical shifts in ab initio solid-state NMR calculations, and the applicability of motional averaging with molecular dynamics has been shown to depend on the accuracy of the molecular mechanical force field. The performance of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base cocaine is used as an example. The results reveal that, even though the TMFF outperforms the COMPASS force field for representing the energies and conformations of predicted structures, it does not give significant improvement in the accuracy of NMR calculations. Further studies should direct more attention to anisotropic chemical shifts and development of the method of solid-state NMR calculations.

Effects of Air Humidity on Properties of JO-9159 Explosive by Molecular Dynamics Simulation

To explore effects of air humidity on properties of JO-9159 explosive, the amorphous model of six components was constructed by Materials Studio software, periodic molecular dynamics simulation was conducted at seven kinds of relative humidity ranging from 10% to 70% for (001), (010), (100) crystal planes of JO-9159 explosive in COMPASS force field and NVT ensemble. Mechanical properties, sensitivity and detonation properties of JO-9159 explosive were researched basing on equilibrium trajectory of model. The results show that with the increasing of relative humidity, the total adsorption energy increases. The adsorption capacity of JO-9159 explosive for H2O is much stronger than O2 and N2; The breaking strength has a decreasing trend with the humidity increases and the stiffness and hardness of JO-9159 explosive are smaller at 30% and 40% relative humidity; At 30% relative humidity, the sensitivity of JO-9159 explosive is highest and detonation properties are weakest, while the detonation properties are strongest at 20% relative humidity.

Determination of the effects of water adsorption on the sensitivity and detonation performance of the explosive JOB-9003 by molecular dynamics simulation.

In order to determine the adsorption mechanism of water on the crystal surfaces of the explosive JOB-9003 and the effect of this adsorption on the sensitivity and detonation performance of this explosive, a model of the crystal of JOB-9003 was created in the software package Materials Studio (MS). The adsorption process was simulated, and molecular dynamics simulation was performed with the COMPASS force field in the NPT ensemble to calculate the sensitivity and detonation performance of the explosive. The results show that the maximum trigger bond length decreases whereas the interaction energy of the trigger bond and the cohesive energy density increase after adsorption, indicating that the sensitivity of JOB-9003 decreases. The results for the detonation performance show that the detonation pressure, detonation velocity, and detonation heat decrease upon the adsorption of water, thus illustrating that the detonation performance of JOB-9003 is degraded. In summary, the adsorption of water has a positive effect on the sensitivity and safety of the explosive JOB-9003 but a negative effect on its detonation performance.

Validation of the COMPASS force field for complex inorganic–organic hybrid polymers

Inorganic–organic hybrid polymers are promising alternatives to simple organic polymers. They combine the advantages of organic and inorganic components in one homogeneous material, which can be adjusted to match sophisticated demands for various possible applications ranging from soft silicones to hard hybrid ceramics. Typically, the inorganic network is formed by a sol-gel reaction whereas the organic network is built by a polymerization reaction. Due to their complex architecture on a molecular level, it is often impossible to experimentally obtain information on the atomistic structures of such hybrid materials. In this work, we validate the all-atom COMPASS force field for the simulation of such materials on the basis of a simplified test system with (methacryloyloxymethyl)dimethylethoxysilane as a precursor; which has only one functionality for inorganic condensation, building only one defined condensation product in the sol-gel reaction. The force field was validated based on the experimentally determined single crystal structure of this condensation product and the calculation of its glass transition and melting temperatures by molecular dynamics. The prediction of fluid densities was validated on liquids of the precursor and the condensation product. The validated force field is applied to demonstrate the influence of inorganic cross-linking in the resulting polymer on a simplified network model.

Microstructure and Properties of Polypropylene/Clay Nanocomposites

ABSTRACTNanocomposites of polypropylene (PP) containing various contents of Cloisite 15A nanoclay particles were prepared by one-step melt compounding in a twin screw extruder. Tensile and impact properties of the nanocomposite systems were investigated and correlated with their microstructures. The tensile modulus increased with an increase in Cloisite 15A content but the tensile strength, elongation at break, and impact strength were decreased. WAXS and TEM studies showed almost exfoliated structures. There was a decrease in permeability values with an increase in nanoclay content up to 5 wt. %. Exceeding this content of nanoclay had no significant effect on permeation due to the aggregation phenomenon at high concentrations of the nanoparticles. Most of the examined micromechanical models for prediction of the tensile modulus of the nanocomposite were successful despite being based on fiber-shaped fillers. An exfoliated structure of clay within the nanocomposite was assumed for the modeling using a molecular dynamics simulations approach, employing Dreiding, Forcite, and COMPASS force fields, in order to investigate the best one for a successful estimation of elastic modulus. Relative to the experimental modulus values of the nanocomposites, which were around 1100–1200 MPa, the COMPASS force field had the best correlation with the values with a slight departure of about 10%.

Thermodynamic and Modeling Study of n-Octane, n-Nonane, and n-Decane Films on MgO(100)

The thermodynamic properties of n-octane, n-nonane, and n-decane adsorbed on the MgO(100) surface were investigated using high-resolution, volumetric adsorption isotherms in the temperature ranges of 225–295, 245–280, and 250–310 K, respectively. Two distinct molecular layers were observed in all isotherms. The heat, differential enthalpy, differential entropy, and isosteric heat of adsorption were determined. The temperature dependence of the two-dimensional compressibility was used to identify that two-phase transitions occur for the first and second layers, respectively. The average area per molecule of 137 ± 5,128 ± 5, and 202 ± 5 A2 for octane, nonane, and decane, respectively, suggests that the carbon backbone is preferentially oriented parallel to the MgO(100) surface. A substantial set of molecular dynamics (MD) temperature and coverage runs for all three molecules using the COMPASS force field were used to calculate both the minimum energy configurations for individual molecules and near-complete...

Computing thermomechanical properties of dry homopolymers used as raw materials for formulation of biomedical hydrogels.

Different static properties have been calculated with COMPASS force field for polyacrylamide, poly(2-hydroxyethylacrylate) (HEA), poly(2-hydroxyethylmethacrylate) (HEMA), poly(glycidylmethacrylate) (GMA), polyethylene glycol (PEG), and poly(2,2,2-trifluoroethylmethacrylate) (TFEM). For each polymers, the calculated values were averaged on five equilibrated configurations of amorphous cell composed of one atactic chain containing 100 repeat units. The ranking obtained from the densities calculated at 300K is TFEM > HEA ≈ xpolycrylamide > HEMA ≈ GMA > PEG. Concerning the glass transition temperature we have obtained polyacrylamide > HEMA ≈ GMA ≈ HEA > PEG, and polyacrylamide > HEMA ≈ HEA > GMA ≈ PEG > TFEM for the bulk modulus. The calculated results, when available, have been compared with experimental data coming from literature.