Condensed-phase Optimized Molecular Potentials For Atomistic Simulation Studies Research Articles

Molecular dynamics study on the microstructure of dendrimers/graphite composites

Abstract

Computational chemistry and molecular simulations of phosphoric acid

AbstractQuantum mechanics (QM) calculations, molecular dynamics (MD) simulations using the condensed‐phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field, and the atom‐centered density matrix propagation (ADMP) approach have been used to investigate properties of phosphoric acid (PA). QM using B3LYP/6‐31++G(d,p) density functional theory were used to calculate gas‐phase proton affinities and interaction energies of PA and its derivatives. Detailed single coordinate driving, followed by quadratic synchronous transit optimization was used to determine energy barriers for different proton transfer (PT) pathways. Determined energy barrier heights in ascending order are (unit: kJ/mol): H3O+→H3PO4 (0); H4P2O7→H3PO4 (2.61); H3PO4→H2PO (5.31); H4PO→H3PO4 (∼7.33); H3PO4→H4P2O7/H3PO4→H3PO4 (15.99); H4P2O7→H2O (28.61); H3PO4→H2O (47.14). The COMPASS force field was used to study condensed‐phase properties of PA. Good agreement between experimental data and MD results including density, radial distribution functions, and self‐diffusion coefficient at different temperatures provides validation of the COMPASS force field for PA. Finally, preliminary ADMP studies on a cluster of three PA molecules shows that the ADMP approach can reasonably describe the PT and self‐dissociation processes in PA. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011

Study of the Mechanical and Thermal Properties of Poly(Lactic Acid) and Poly(Ethylene Glycol) Block Copolymer with Molecular Dynamics

In this study, the mechanical properties and glass transition temperature of PLA-PEG block copolymer were investigated by molecular dynamic simulation. The software package Discover in Materials Studio with condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field was used for the simulation. To verify the validity of simulation results, PLA and PLA-PEG copolymer were prepared in this research and the glass transition temperature was measured by DSC. The simulation results showed that the random combination chain has more probability than the alternating combination chain to exist in copolymer structure. Furthermore, PLA-PEG block copolymer has better tensile strength but lower shear strength than PLA, which agree well with the theoretical results. The simulation values of Tg (PLA: 333.97 K and PLA-PEG: 326.70 K) agree well with the DSC results (PLA: 328.8 K and PLA-PEG: 321.3 K). The conclusion could be drawn from the results that molecular dynamic simulation (MDS) is a potential method for investigating the structure, mechanical properties, and glass transition temperature of PLA-PEG copolymer and may be used for other polymers and copolymers.

Study on the gas permeabilities in styrene-butadiene rubber by molecular dynamics simulation

In this research, molecular dynamics (MD) simulations were used to study the transport properties of small gas molecules in the butadiene-styrene copolymer (SBR). The condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field was applied. The diffusion coefficients were obtained from MD (NVT ensemble) and the relationship between gas permeability; the chemical structure and free volume of butadiene-styrene copolymer were investigated. The results indicated that the diffusion coefficient of oxygen declined with increasing styrene content. The fraction of free volume (FFV) in butadiene-styrene copolymer was calculated. It was concluded that diffusion coefficient increased as the FFV increases, which is in accordance with the analysis of the small molecular hop through the free volume in polymer matrix. Subsequently, the glass transition temperatures of these copolymers were calculated by MD. The result showed that the glass transition temperature increased with increasing styrene content in polymer.

Study of the dynamics of poly(ethylene oxide) by combining molecular dynamic simulations and neutron scattering experiments

We performed quasielastic neutron scattering experiments and atomistic molecular dynamics simulations on a poly(ethylene oxide) (PEO) homopolymer system above the melting point. The excellent agreement found between both sets of data, together with a successful comparison with literature diffraction results, validates the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field used to produce our dynamic runs and gives support to their further analysis. This provided direct information on magnitudes which are not accessible from experiments such as the radial probability distribution functions of specific atoms at different times and their moments. The results of our simulations on the H-motions and different experiments indicate that in the high-temperature range investigated the dynamics is Rouse-like for Q-values below approximately 0.6 A(-1). We then addressed the single chain dynamic structure factor with the simulations. A mode analysis, not possible directly experimentally, reveals the limits of applicability of the Rouse model to PEO. We discuss the possible origins for the observed deviations.

Molecular Simulation of Water/Alcohol Mixtures’ Adsorption and Diffusion in Zeolite 4A Membranes

The COMPASS (condensed-phase optimized molecular potentials for atomistic simulation studies) force field with two sets of partial atomic charges of water was used to simulate adsorption and diffusion behavior of water/methanol and water/ethanol mixtures in zeolite 4A at 298 K. The adsorption of alcohol first increased and then decreased with increasing pressure, whereas the adsorption of water increased progressively until an adsorption equilibrium was reached. Both the adsorbed molecules and the zeolite framework were treated as a fully flexible model in MD simulations. The simulation results show that the effects of the size and steric hindrance of the diffusing molecules on diffusivity are significant. The diffusivity of water, methanol, and ethanol molecules decreases by 1 order of magnitude in the order of water > methanol > ethanol. The diffusivity of water molecules depends on the mass fraction and the partial charges of water in zeolite 4A. The ethanol and methanol molecules have restricted motion through the alpha-cages, whereas the water molecules can easily pass through the alpha-cages window at low feed alcohol concentrations. And the extent of hydrogen bonding increased with increasing water concentration.

THE STUDY ON THE GAS PERMEABILITIES OF THE ETHYLENE/1-HEXENE COPOLYMER BY MOLECULAR DYNAMICS SIMULATION

In this research, molecular dynamics(MD) simulations were used to study the transport properties of small gas molecules in poly(ethylene-co-1-hexene) copolymer. The condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) forcefield was applied. The diffusion coefficients were obtained from MD (NVT ensemble). The results indicated that the diffusion coefficient of oxygen increased with increasing 1-hexene content in copolymer membrane.

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.

Transport Behavior of Oxygen and Nitrogen through Organasilicon-Containing Polystyrenes by Molecular Simulation

Molecular dynamics (MD) simulations have been used to study the transport properties of oxygen and nitrogen in the para-substituted polystyrenes which possess one to four Si atoms in each substituent. The Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies (COMPASS) force field was used to construct the polymers. Diffusion coefficients were obtained from molecular dynamics (NVT ensemble) with up to 3 ns simulation times. After molecular dynamic simulation, the trajectories of the small molecules in the polymer matrix were obtained. Then diffusion coefficients have been calculated from the Einstein relationship revealing a considerable agreement between the simulated and the experimental data. And solubility coefficients have been calculated by the Grand Canonical Monte Carlo (GCMC) method. The solubility of oxygen increased with increasing Si content in the polymer membrane. The para-substituted polystyrenes with a branched substituent at the alpha-position showed higher permeability than those of the nonbranched ones. The higher the glass transition temperature (T(g)) of the membrane, the larger the diffusion coefficients of oxygen and nitrogen obtained.

Molecular dynamics study of the effect of solvent types on the dynamic properties of polymer chains in solution

The effect of types of solvent on the dynamic properties of atactic poly(methyl methacrylate)s (a-PMMA)s chains in solution was studied by a molecular dynamics simulation technique with the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field. Five kinds of casting solvent molecules were randomly embedded into the a-PMMA matrix to construct various types of simulated a-PMMA solutions based upon experimentally obtained densities. The dynamic properties of polymer chains such as mean-square end-to-end distance < R 2 >, mean-square radius of gyration < S 2 >, and asphericity ratio < R 2 >/< S 2 > of polymer chains were analyzed. Simulated results revealed that the < R 2 > of the a-PMMA chains increased with the increase of the dipole moment of the surrounded solvent molecules. The asphericity ratio of polymer chains showed a high correlation to the molecular weight of solvents. Furthermore, the simulated radial distribution function of H-H atomic pairs in the system of a-PMMA solutions indicated that the expansion of a polymer chain depends mainly on the conformation of solvent molecules instead of the interaction between the polymer chain and the functional group on solvent molecules.

One-to-one reactant–modifier interactions in enantio- and diastereoselective hydrogenation of chiral α-hydroxyketones on Pt(111)

Hydrogen-bonding interactions between α-hydroxyketones (i.e., ( R)- and ( S)-1-hydroxy-1-phenyl-2-propanones and ( R)- and ( S)-2-hydroxy-1-phenyl-1-propanones) and protonated cinchonidine in Open(3) conformation relevant to enantioselective hydrogenation over Pt were studied computationally at the B3LYP/TZVP level. The density functional theory (DFT)-optimized structures were reoptimized on a flat Pt(111) surface with molecular mechanics using the condensed phase-optimized molecular potentials for atomistic simulation studies (COMPASS) force field. Two possible interaction modes—the so-called bifurcated and cyclic hydrogen bonded complexes—were studied. In the former, both oxygens of the reactant interact with the proton attached to the modifier's quinuclidine nitrogen; in the latter, one modifier's hydroxyl group also interacts with the substrate's oxygen. Bifurcated complexes were found to be 3–8 kJ mol −1 more stable than the cyclic complexes by DFT calculations. By the force field calculations, only three cyclic complexes relevant to the reaction were found to be stable on the Pt(111) surface, and they were less stable than the bifurcated complexes. Thus, the relevance of the cyclic complexes between α-hydroxyketones and cinchonidine to enantiodifferentiation can be considered negligible. Furthermore, no bifurcated but single hydrogen bonded complexes were found to be stable on the Pt(111) surface for 1-hydroxy-1-phenyl-2-propanones with an sp 3-hybridized carbon next to the phenyl ring. DFT calculations indicated that complexes leading to ( R)-stereoisomers were more thermodynamically stable than the complexes leading to ( S)-stereoisomers. In general, orbital analysis of the reacting C O keto carbonyl orbitals indicated that formation of ( R)-stereoisomers was kinetically preferred as well. However, DFT calculations of isolated complexes cannot qualitatively predict the enantiomeric excess, requiring that the steric restriction of the Pt surface be taken into account. By combining the results of DFT and force field calculations, a reasonable explanation for experimentally observed product distribution was obtained.

A molecular dynamics simulation of the melting points and glass transition temperatures of myo- and neo-inositol

The heat of sublimation, density, melting point, and glass transition temperature are calculated for myo- and neo-inositol, using the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field and molecular dynamics techniques. Our results show that the calculated heats of sublimation and density are very close to the experimental values for both compounds. Furthermore, our simulated melting temperatures for myo- and neo-inositol also compare very well to the experimentally obtained data. The glass transition temperatures for myo- and neo-inositol have been calculated to be ca. 494 K and ca. 518 K, respectively, and the shape of the volume versus temperature plots produced are typical for a glass transition. As a result, it is our view that the COMPASS force field suitably describes these two compounds in molecular simulations and that molecular dynamics techniques, combined with this force field, can be used to simulate the melt and glass transitions for such molecules.

Molecular simulation of the glass transition of polyphosphazenes

Molecular dynamics simulation (NPT ensemble) has been used to obtain specific volume as a function of temperature for four polyphosphazenes. From these results, the volumetric glass transition temperature has been determined as the temperature marking the discontinuity in slope of the V–T simulation data. The molecular mechanics force field used in this study was COMPASS (Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies) which has been extensively parameterized and validated for phosphazenes in a previous communication. The polyphosphazenes include poly[bis(2,2,2-trifluoroethoxy)phosphazene] (PTFEP) and three isomers of poly(dibutoxyphosphazene)—poly[bis(n-butoxy)phosphazene] (PnBuP), poly[bis(iso-butoxy)phosphazene)] (PiBuP), and poly[bis(sec-butoxy)phosphazene] (PsBuP). In all cases, there was reasonable agreement between experimental results and values of density and Tg obtained from the simulations. In the case of PnBuP, two different methods for amorphous cell building are compared to explore the relationship between the state of equilibration and the Tg obtained from simulation.