Mesoscale model of polymer melt structure: self-consistent mapping of molecular correlations to coarse-grained potentials

Development and application of coarse-graining methods to condensed phases of macromolecules is an active area of research. Multiscale modeling of polymeric systems using coarse-graining methods presents unique challenges. Here we apply a coarse-graining method that self-consistently maps structural correlations from detailed molecular dynamics (MD) simulations of alkane oligomers onto coarse-grained potentials using a combination of MD and inverse Monte Carlo methods. Once derived, the coarse-grained potentials allow computationally efficient sampling of ensemble of conformations of significantly longer polyethylene chains. Conformational properties derived from coarse-grained simulations are in excellent agreement with experiments. The level of coarse graining provides a control over the balance of computational efficiency and retention of chemical identity of the underlying polymeric system. Challenges to extension and application of this and similar structure-based coarse-graining methods to model dynamics and phase behavior in polymeric systems are briefly discussed.     

Development and validation of an integrated computational approach for the study of ionic species in solution by means of effective two-body potentials. The case of Zn2+, Ni2+, and Co2+ in aqueous solutions

In this paper we have developed an effective computational procedure for the structural and dynamical investigation of ions in aqueous solutions. Quantum mechanical potential energy surfaces for the interaction of a transition metal ion with a water molecule have been calculated taking into account the effect of bulk solvent by the polarizable continuum model (PCM). The effective ion-water interactions have been fitted by suitable analytical potentials, and have been utilized in molecular dynamics (MD) simulations to obtain structural and dynamical properties of the ionic aqueous solutions. This procedure has been successfully applied to the Co2+-H2O open-shell system and, for the first time, Co-oxygen and Co-hydrogen pair potential functions have been determined and employed in MD simulations. The reliability of the whole procedure has been assessed by applying it also to the Zn2+ and Ni2+ aqueous solutions, and the structural and dynamical properties of the three systems have been calculated by means of MD simulations and have been found to be in very good agreement with experimental results. The structural parameters of the first solvation shells issuing from the MD simulations provide an effective complement to extended X-ray absorption fine structure (EXAFS) experiments.     

Atomistic simulations to compute surface properties of poly(N-vinyl-2-pyrrolidone) (PVP) and blends of PVP/chitosan

Atomistic simulations were performed on poly(N-vinyl-2-pyrrolidone) (PVP) and its blends with chitosan (CS) in different ratios using molecular mechanics (MM) and molecular dynamics (MD) simulations in three-dimensionally periodic and effective two-dimensionally periodic condensed phases. Four independent microstructures were generated to analyze their surface properties. The calculated surface-energy values for PVP compared quite well with the experimental data reported in the literature. The density profile was analyzed, and the structure of the films showed an interior region of the bulk density. Various components of the energetic interactions (torsional, van der Waals, etc.) were examined to gain deeper insight into the nature of regular and anomalous interactions between the bulk and the surface films. Surface energies of PVP/CS blends were computed by MD simulations using the bulk pressure-volume-temperature (PVT) parameters. Bulk properties such as the cohesive energy density (CED) and solubility parameter (delta) were calculated using MM and MD simulations in the NVT ensemble under periodic boundary conditions. The Flory equation of state was used to compute the thermal expansion coefficient as well as PVT parameters. These surface-energy values agreed well with the surface-energy data calculated using the Zisman equation, which were also in accordance with the experimental observations. The results from this study suggest that computer simulations would provide valuable information on polymers and polymer-blend surfaces.     

The nature of the calculation of the pressure in molecular simulations of continuous models from volume perturbations

We consider some fundamental aspects of the calculation of the pressure from simulations by performing volume perturbations. The method, initially proposed for hard-core potentials by Eppenga and Frenkel [Mol. Phys.52, 1303 (1984)] and then extended to continuous potentials by Harismiadis et al. [J. Chem. Phys. 105, 8469 (1996)], is based on the numerical estimate of the change in Helmholtz free energy associated with the perturbation which, in turn, can be expressed as an ensemble average of the corresponding Boltzmann factor. The approach can be easily generalized to the calculation of components of the pressure tensor and also to ensembles other than the canonical ensemble. The accuracy of the method is assessed by comparing simulation results obtained from the volume-perturbation route with those obtained from the usual virial expression for several prototype fluid models. Monte Carlo simulation data are reported for bulk fluids and for inhomogeneous systems containing a vapor-liquid interface.     

Understanding mixing of Ni and Pt in the Ni/Pt(111) bimetallic catalyst via molecular simulation and experiments

Molecular dynamics (MD) simulations employing embedded atom method potentials and ultrahigh vacuum (UHV) experiments were carried out to study the mixing process between the Ni and Pt atoms in the Ni/Pt(111) bimetallic system. The barrier for a Ni atom to diffuse from the top surface to the subsurface layer is rather high (around 1.7 eV) as calculated using the nudged elastic band (NEB) method. Analysis of the relaxation dynamics of the Ni atoms showed that they undergo diffusive motion through a mechanism of correlated hops. At 600 K, all Ni atoms remain trapped on the top surface due to large diffusion barriers. At 900 K, the majority of Ni atoms diffuse to the second layer and at 1200 K diffusion to the bulk is observed. We also find that smaller Ni coverages and the presence of Pt steps facilitate the Ni-Pt mixing. By simulated annealing simulations, we found that in the mixed state, the Ni fraction oscillates between layers, with the second layer being Ni-richer at equilibrium. The simulation results at multiple time scales are consistent with the experimental data.     

A powerful computational crystallography method to study ice polymorphism

Classical molecular dynamics (MD) simulations are employed as a tool to investigate structural properties of ice crystals under several temperature and pressure conditions. All ice crystal phases are analyzed by means of a computational protocol based on a clustering approach following standard MD simulations. The MD simulations are performed by using a recently published classical interaction potential for oxygen and hydrogen in bulk water, derived from neutron scattering data, able to successfully describe complex phenomena such as proton hopping and bond formation/breaking. The present study demonstrates the ability of the interaction potential model to well describe most ice structures found in the phase diagram of water and to estimate the relative stability of 16 known phases through a cluster analysis of simulated powder diagrams of polymorphs obtained from MD simulations. The proposed computational protocol is suited for automated crystal structure identification.     

Molecular dynamics simulation of surface segregation in a (110) B2-NiAl thin film

Surface segregation in (110) B2-NiAl film approximately 3 nm thick is investigated by using molecular dynamics simulation with a reliable embedded-atom potential. The simulation is performed for the stoichiometric composition at a temperature of 1500 K, just below the melting temperature of the film model. It is found that the (110) surface is structurally stable but develops adatoms, vacancies and antisites. The coverage of an adatom layer is estimated to be ～0.07 ML (monatomic layers) and it contains on average ～95% of Al atoms. The top (surface) and second (subsurface) layers of the (110) surface is the most enriched in Ni relative to the bulk composition. These layers contain on average ～51% of Ni atoms. The Ni fraction in the third and forth layers of the film is estimated as ～50.5%. The deeper layers have essentially the bulk composition. Vacancies in the film model are found only on the Ni sublattice. The vacancy concentration on the Ni sublattice in the top layer is ～7.5%. The second layer almost does not contain vacancies. The next layers have essentially the constant bulk vacancy composition which can be estimated as ～1.3-1.4%.     

Thermodynamics and partitioning of homopolymers into a slit-A grand canonical Monte Carlo simulation study

Grand canonical ensemble Monte Carlo simulation (GCMC) combined with the histogram reweighting technique was used to study the thermodynamic equilibrium of a homopolymer solution between a bulk and a slit pore. GCMC gives the partition coefficients that agree with those from canonical ensemble Monte Carlo simulations in a twin box, and it also gives results that are not accessible through the regular canonical ensemble simulation such as the osmotic pressure of the solution. In a bulk polymer solution, the calculated osmotic pressure agrees very well with the scaling theory predictions both for the athermal polymer solution and the theta solution. However, one cannot obtain the osmotic pressure of the confined solution in the same way since the osmotic pressure of the confined solution is anisotropic. The chemical potentials in GCMC simulations were found to differ by a translational term from the chemical potentials obtained from canonical ensemble Monte Carlo simulations with the chain insertion method. This confirms the equilibrium condition of a polymer solution partition between the bulk and a slit pore: the chemical potentials of the polymer chain including the translational term are equal at equilibrium. The histogram reweighting method enables us to obtain the partition coefficients in the whole range of concentrations based on a limited set of simulations. Those predicted bulk-pore partition coefficient data enable us to perform further theoretical analysis. Scaling predictions of the partition coefficient at different regimes were given and were confirmed by the simulation data.     

Phase separation in binary mixtures containing polymers: A quantitative comparison of single-chain-in-mean-field simulations and computer simulations of the corresponding multichain systems

We discuss a phenomenological, coarse-grained simulation scheme, single-chain-in-mean-field (SCMF) simulation, for investigating the kinetics of phase separation in dense polymer blends and mixtures of polymers and solvents. In the spirit of self-consistent-field calculations, we approximate the interacting multichain problem by that of a single chain in an external field, which, in turn, depends on the local densities of the components. To study the time evolution of the mixture, we perform an explicit Monte Carlo (MC) simulation of an ensemble of independent chains in the external field and periodically calculate the average densities and update the external field. Unlike dynamic self-consistent-field theory, these SCMF simulations do not assume that the chain conformations relax much more quickly than the density and incorporate the single-chain dynamics explicitly rather than via an Onsager coefficient. This allows us to study systems with large spatial inhomogeneities and dynamic asymmetries. To assess the accuracy and limitations of the simulation scheme, we compare the results of SCMF simulations using a discretized Edwards Hamiltonian with computer simulations of the corresponding multichain system for (1) the early stages of spinodal decomposition of a symmetric binary polymer blend in response to a quench from χN = 0.314 to χN = 5 (where χ is the Flory–Huggins parameter and N is the number of segments), for which the growth rate of composition fluctuations is compared with MC simulations of the bond fluctuation model and alternative dynamic self-consistent-field calculations, and (2) the evaporation of a solvent from a low-molecular-weight thin polymer film, for which a comparison is made with molecular dynamics (MD) simulations of a bead-necklace model with a monomeric solvent. In the latter case, the polymer conformations are extracted from MD simulations and modeled in the SCMF simulations by a discretized Edwards Hamiltonian augmented by a chain-bending potential. From the MD simulations of thin polymer films in equilibrium with its vapor, phase coexistence has been determined, and the second- and third-order virial coefficients in the SCMF simulations have been adjusted accordingly. Finally, MD simulations of bulk solutions of a polymer and a solvent over a range of compositions, as well as the pure solvent at various densities, have been performed to determine self-diffusion coefficients that enter the SCMF simulations in the form of density-dependent segmental mobilities. A comparison of the polymer and solvent profiles in a thin film as a function of time and the fraction of the solvent evaporating from a solvent-swollen film, as obtained from MD simulations and parameterized SCMF simulations, shows satisfactory agreement for this simple mapping procedure. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 934–958, 2005     

Reactive Monte Carlo and grand-canonical Monte Carlo simulations of the propene metathesis reaction system

The influence of silicalite-1 pores on the reaction equilibria and the selectivity of the propene metathesis reaction system in the temperature range between 300 and 600 K and the pressure range from 0.5 to 7 bars has been investigated with molecular simulations. The reactive Monte Carlo (RxMC) technique was applied for bulk-phase simulations in the isobaric-isothermal ensemble and for two phase systems in the Gibbs ensemble. Additionally, Monte Carlo simulations in the grand-canonical ensemble (GCMC) have been carried out with and without using the RxMC technique. The various simulation procedures were combined with the configurational-bias Monte Carlo approach. It was found that the GCMC simulations are superior to the Gibbs ensemble simulations for reactions where the bulk-phase equilibrium can be calculated in advance and does not have to be simulated simultaneously with the molecules inside the pore. The confined environment can increase the conversion significantly. A large change in selectivity between the bulk phase and the pore phase is observed. Pressure and temperature have strong influences on both conversion and selectivity. At low pressure and temperature both conversion and selectivity have the highest values. The effect of confinement decreases as the temperature increases.     

Modelling a nematic liquid crystal

The bulk phase liquid crystalline behaviour of a cyclic siloxane with a pentamethylcyclosiloxane core and biphenyl-4-allyloxybenzoate mesogens (BCS) was studied using molecular dynamics (MD) and wide angle X-ray analysis. This material exhibits partial crystallinity at room temperature and liquid crystalline behaviour above 120° C. For the MD simulations an ensemble of 27 molecules with 135 mesogenic units was simulated and a molecular mechanics force field was used to model the structural anisotropy of the siloxane molecules. Simulations were carried out both at room temperature and at an elevated temperature (425 K). Room temperature simulations showed that, contrary to our initial assumptions, the low energy molecular conformations were not cylindrical but splayed in shape. During the simulation a smectic-like, tilted layer structure was found to evolve for the cluster when full atom potentials were used, while no such development was observed when electrostatic interactions were neglected. The presence of a tilted layered structure was also suggested by the X-ray data. These results indicate that long range electrostatic interactions are significant for the molecular system under study. In order to calculate the orientational order parameter, the orientation of the molecular axis had to be determined. This was achieved by describing the mesogen shapes to be ellipsoidal and defining the principal axis of the ellipsoids to be the molecular directors. By sampling over 200 ps of simulation at 425 K, the time averaged order parameter (S) was calculated. The calculated S of 0.36 was comparable to the value of 0.4-0.45 found from the experimental data. Apart from providing insight into the relative importance of the various competing forces in the formation of the liquid crystalline phase, these simulations are also expected to be useful in predicting the mesophase behaviour of liquid crystalline systems.     

Insights into uranyl chemistry from molecular dynamics simulations

First-principles and purely classical molecular dynamics (MD) simulations for complexes of the uranyl ion (UO(2)(2+)) are reviewed. Validation of Car-Parrinello MD simulations for small uranyl complexes in aqueous solution is discussed. Special attention is called to the mechanism of ligand-exchange reactions at the uranyl centre and to effects of solvation and hydration on coordination and structural properties. Large-scale classical MD simulations are surveyed in the context of liquid-liquid extraction, with uranyl complexes ranging from simple hydrates to calixarenes, and nonaqueous phases from simple organic solvents and supercritical CO(2) to ionic liquids.     

An elegant access to formation and vaporization enthalpies of ionic liquids by indirect DSC experiment and "in silico" calculations

We used DSC for determination of the reaction enthalpy of the synthesis of the ionic liquid [C(4)mim][Cl]. A combination of DSC and quantum chemical calculations presents a new, indirect way to study thermodynamics of ionic liquids. The new procedure was validated with two direct experimental measurements and MD simulations.     

Exploring the Effects of Ionic Defects on the Stability of CsPbI3 with a Deep Learning Potential

Inorganic metal halide perovskites, such as CsPbI₃, have recently drawn extensive attention due to their excellent optical properties and high photoelectric efficiencies. However, the structural instability originating from inherent ionic defects leads to a sharp drop in the photoelectric efficiency, which significantly limits their applications in solar cells. The instability induced by ionic defects remains unresolved due to its complicated reaction process. Herein, to explore the effects of ionic defects on stability, we develop a deep learning potential for a CsPbI₃ ternary system based upon density functional theory (DFT) calculated data for large-scale molecular dynamics (MD) simulations. By exploring 2.4 million configurations, of which 7,730 structures are used for the training set, the deep learning potential shows an accuracy approaching DFT-level. Furthermore, MD simulations with a 5,000-atom system and a one nanosecond timeframe are performed to explore the effects of bulk and surface defects on the stability of CsPbI₃. This deep learning potential based MD simulation provides solid evidence together with the derived radial distribution functions, simulated diffraction of X-rays, instability temperature, molecular trajectory, and coordination number for revealing the instability mechanism of CsPbI₃. Among bulk defects, Cs defects have the most significant influence on the stability of CsPbI₃ with a defect tolerance concentration of 0.32 %, followed by Pb and I defects. With regards to surface defects, Cs defects have the largest impact on the stability of CsPbI₃ when the defect concentration is less than 15 %, whereas Pb defects act play a dominant role for defect concentrations exceeding 20 %. Most importantly, this machine-learning-based MD simulation strategy provides a new avenue to explore the ionic defect effects on the stability of perovskite-like materials, laying a theoretical foundation for the design of stable perovskite materials.     

Thermodynamics of the liquid states of Langmuir monolayers

The liquid states and the liquid-liquid equilibrium of surfactant molecules forming an interphase between air and water have been considered using Monte Carlo computer simulations. Specifically, the expanded and compressed liquid phases observed for surfactant molecules were characterized as a function of pressure and temperature. Simple modified beadlike potentials were implemented in order to describe the interparticle forces between the hydrophobic and hydrophilic portions of surfactant molecules at the air/water interface. A simulation box was defined such that the monolayer was exposed to an externally applied lateral pressure in a modified isothermal-isobaric ensemble, whereas the water bath was modeled in a canonical ensemble. The simulation resembles the experimental setup used to measure lateral pressure (Pi) versus area isotherms obtained with Langmuir troughs. The applied lateral pressure-surface area phase diagram clearly showed the coexistence of the expanded and compressed liquid phases within certain temperature and pressure ranges. Distribution functions of distances and enthalpies for the monolayer were computed to clearly identify each liquid phase and the coexistence region.     

镍铝介金属镀膜之抗坑蚀行为

采用3种原子百分比Ni52Al48,Ni60Al40及Ni70Al30成分的靶材以阴极电弧放电离子被覆技术制备不同组成的Ni＿Al薄膜于AISI1045中碳钢基材表面上,并观察镀膜微结构与成分随靶材成分的变化,评估应用Ni＿Al于抗坑蚀功能方面的可行性.研究结果显示:使用上述3种靶材所获致的镀膜组成依次为Ni62Al38,Ni63Al37及Ni69Al31,镀膜镍含量随靶材镍含量增加而增加.3种镀膜的相组成均以Ni3Al为主,从富镍Ni70Al30靶材所得的镀膜尚含有部分镍相.镀膜具有极强的附着性并反映在镀膜的抗坑蚀性上.在纯水中,所有的Ni＿Al镀膜试片均能提高中碳钢基材的抗坑蚀性,约达10倍.在3.5wt%盐水与3.5wt%盐酸中亦分别有两倍以上的效果.而在这3种测试环境中,3种镀膜试片的坑蚀损失差别均不明显,无法判断镀膜组成对抗坑蚀性的影响.从动电位极化曲线可以看出,镀膜试片均能大幅提高基材在盐酸与盐水溶液中的抗蚀性,然而因坑蚀破坏而形成的孔洞会由于孔蚀而导致腐蚀加剧,造成镀膜试片在腐蚀溶液中之抗坑蚀效果低于电化学量测时所预期的保护效果.     

The [BMI][Tf2N] ionic liquid/water binary system: a molecular dynamics study of phase separation and of the liquid-liquid interface

We report molecular dynamics (MD) simulations of the aqueous interface of the hydrophobic [BMI][Tf2N] ionic liquid (IL), composed of 1-butyl-3-methylimidazolium cations (BMI+) and bis(trifluoromethylsulfonyl)imide anions (Tf2N-). The questions of water/IL phase separation and properties of the neat interface are addressed, comparing different liquid models (TIP3P vs TIP5P water and +1.0/-1.0 vs +0.9/-0.9 charged IL ions), the Ewald vs the reaction field treatments of the long range electrostatics, and different starting conditions. With the different models, the "randomly" mixed liquids separate much more slowly (in 20 to 40 ns) than classical water-oil mixtures do (typically, in less than 1 ns), finally leading to distinct nanoscopic phases separated by an interface, as in simulations which started with a preformed interface, but the IL phase is more humid. The final state of water in the IL thus depends on the protocol and relates to IL heterogeneities and viscosity. Water mainly fluctuates in hydrophilic basins (rich in O(Tf2N) and aromatic CH(BMI) groups), separated by more hydrophobic domains (rich in CF3(Tf2N) and alkyl(BMI) groups), in the form of monomers and dimers in the weakly humid IL phase, and as higher aggregates when the IL phase is more humid. There is more water in the IL than IL in water, to different extents, depending on the model. The interface is sharper and narrower (approximately 10 A) than with the less hydrophobic [BMI][PF6] IL and is overall neutral, with isotropically oriented molecules, as in the bulk phases. The results allow us to better understand the analogies and differences of aqueous interfaces with hydrophobic (but hygroscopic) ILs, compared to classical organic liquids.