A study on the relationship between polycarbonate microstructure and performance as determined by a combined experimental and molecular dynamics simulation method

The influence of structure of poly(bisphenol-A carbonate) on property was systematically studied by both experiment and molecular dynamic simulation. At the molecular level, it was observed that copolymerisation of dichlorodimethylsilane did not improve the thermal stability and optical property, through 13C-nuclear magnetic resonance. Molecular simulation has good agreement with experimental results on density, half decomposition temperature (T1/2), glass transition temperature (Tg), refraction index, flow activation energy and mechanical performance. The molecular dynamics results demonstrated the feasibility of molecular simulation technique in designing materials at the molecular scale, and had advantage in improving our understanding of material’ performance and pressure–volume–temperature characteristics. The pressure–volume–temperature dependences of different microstructure amorphous were characterised to optimise the processing parameters, and to obtain accurate prediction of material's property. The empirical Tait equation of state well described the pressure–volume–temperature dependence of amorphous liquids.

The virial stress is the most commonly used definition of stress in discrete particle systems. This quantity includes two parts. The first part depends on the mass and velocity (or, in some versions, the fluctuation part of the velocity) of atomic particles, reflecting an assertion that mass transfer causes mechanical stress to be applied on stationary spatial surfaces external to an atomic‐particle system. The second part depends on interatomic forces and atomic positions, providing a continuum measure for the internal mechanical interactions between particles. Historic derivations of the virial stress include generalization from the virial theorem of Clausius (1870) for gas pressure and solution of the spatial equation of balance of momentum. The virial stress is stress‐like a measure for momentum change in space. This paper shows that, contrary to the generally accepted view, the virial stress is not a measure for mechanical force between material points and cannot be regarded as a measure for mechanical stress in any sense. The lack of physical significance is both at the individual atom level in a time‐resolved sense and at the system level in a statistical sense. It is demonstrated that the interatomic force term alone is a valid stress measure and can be identified with the Cauchy stress. The proof in this paper consists of two parts. First, for the simple conditions of rigid translation, uniform tension and tension with thermal oscillations, the virial stress yields clearly erroneous interpretations of stress. Second, the conceptual flaw in the generalization from the virial theorem for gas pressure to stress and the confusion over spatial and material equations of balance of momentum in theoretical derivations of the virial stress that led to its erroneous acceptance as the Cauchy stress are pointed out. Interpretation of the virial stress as a measure for mechanical force violates balance of momentum and is inconsistent with the basic definition of stress. The versions of the virial‐stress formula that involve total particle velocity and the thermal fluctuation part of the velocity are demonstrated to be measures of spatial momentum flow relative to, respectively, a fixed reference frame and a moving frame with a velocity equal to the part of particle velocity not included in the virial formula. To further illustrate the irrelevance of mass transfer to the evaluation of stress, an equivalent continuum (EC) for dynamically deforming atomistic particle systems is defined. The equivalence of the continuum to discrete atomic systems includes (i) preservation of linear and angular momenta, (ii) conservation of internal, external and inertial work rates, and (iii) conservation of mass. This equivalence allows fields of work‐ and momentum‐preserving Cauchy stress, surface traction, body force and deformation to be determined. The resulting stress field depends only on interatomic forces, providing an independent proof that as a measure for internal material interaction stress is independent of kinetic energy or mass transfer.

The mobility of simple ions such as alkali–metal and halide ions at room temperature shows two anomalies. Firstly, there are maxima in mobilities as a function of ion size for both positive and negative ions and, secondly, the maximum for negative ions occurs at a larger ionic radius than the maximum for positive ions. Theoretical treatments of this problem are reviewed and it is concluded that a molecular treatment of the system is needed to understand the results. Computer simulation using the simple point charge model (SPC/E) for water reproduced the observations and is used to discuss the application of theories. In particular, the nature of the first solvation shell is correlated with ion mobility. Simulation reveals a further anomaly, namely that if the charge is removed from a large ion, then it moves more slowly. This is interpreted as the result of formation of a solvent cage around the hydrophobic solute. The changes in local structure resulting from changes in charge and size also affect the solvation thermodynamics. Simulations show that the solvation entropy has a double maximum when viewed as a function of charge. The local minimum near zero charge is interpreted as being due to hydrophobic order, and the maxima as the result of structure breaking. This double maximum in the entropy of solvation is a signature of the hydrophobic cage effect. Comparisons are made between ion mobilities in liquid water at ambient and supercritical conditions.

Chemical penetration enhancers (CPEs) are commonly added into transdermal patches to impart improved skin permeation of drug. However, significant unexplained variability in drug release kinetics in transdermal patches is possible as a result of the addition of CPEs; investigations into the underlying mechanisms are still limited. In the present study, a diverse set of CPEs was employed to draw broad conclusions. Solubility parameters of CPEs and acrylate pressure-sensitive adhesive were calculated by molecular dynamics simulation and Fedors group contribution method to evaluate drug-adhesive miscibility. CPE-adhesive interaction was characterized by FT-IR study, 13C NMR spectroscopy, and molecular docking simulation. Results showed that release enhancement ratio (ERR) of CPEs for zolmitriptan was rank ordered as isopropyl myristate > azone > Plurol Oleique® CC497 > Span® 80 > N-methylpyrrolidone > Transcutol® P. It was found that solubility parameter difference (Δδ) between CPE and adhesive was negatively related with ERR. It was proved that hydrogen bonding between CPE and adhesive would increase drug release rate, but only if the CPE showed good miscibility with adhesive. CPE like isopropyl myristate, which had good miscibility with adhesive, could decrease drug-adhesive interaction leading to the release of drug from adhesive.

An investigation of the relationship between the microstructure parameters and thermomechanical properties of epoxy resin can provide a scientific basis for the optimization of epoxy systems. In this paper, the thermomechanical properties of diglycidyl ether of bisphenol A (DGEBA)/methyl tetrahydrophthalic anhydride (MTHPA) and DGEBA/nadic anhydride (NA) were calculated and tested by the method of molecular dynamics (MD) simulation combined with experimental verification. The effects of anhydride curing agents on the thermomechanical properties of epoxy resin were investigated. The results of the simulation and experiment showed that the thermomechanical parameters (glass transition temperature (Tg) and Young’s modulus) of the DGEBA/NA system were higher than those of the DGEBA/MTHPA system. The simulation results had a good agreement with the experimental data, which verified the accuracy of the crosslinking model of epoxy resin cured with anhydride curing agents. The microstructure parameters of the anhydride-epoxy system were analyzed by MD simulation, including bond-length distribution, synergy rotational energy barrier, cohesive energy density (CED) and fraction free volume (FFV). The results indicated that the bond-length distribution of the MTHPA and NA was the same except for C–C bonds. Compared with the DGEBA/MTHPA system, the DGEBA/NA system had a higher synergy rotational energy barrier and CED, and lower FFV. It can be seen that the slight change of curing agent structure has a significant effect on the synergy rotational energy barrier, CED and FFV, thus affecting the Tg and modulus of the system.

Study of the interfacial array behaviour of surfactant at very low concentration by second harmonic generation and molecular dynamic simulation

Potential energy surfaces (PES) are crucial to the study of reactive and nonreactive chemical systems by Monte Carlo (MC) or molecular dynamics (MD) simulations. Ideally, PES should have the accuracy provided by ab initio calculations and be set up as fast as possible. Recently, neural networks (NNs) turned out as a suitable approach for estimating PES from ab initio/DFT energy datasets. However, the accuracy of the properties determined by MC and MD simulation methods from NNs surfaces has not yet, to our knowledge, been systematically analyzed in terms of the minimum number of energy points required for training and the usage of different NN‐types. The goal of this work is to train NNs for reproducing PES represented by well‐known analytical potential functions, and then to assess the accuracy of the method by comparing the simulation results obtained from NNs and analytical PES. Ensembles of feed‐forward neural networks (EnsFFNNs) and associative neural networks (ASNNs) are used to estimate the full energy surface. Training sets with different number of points, from 15 differently parameterized Lennard–Jones (LJ) potentials, are used and argon is taken to test the network. MD simulations have been performed using the tabular potential energies, predicted by NNs, for working out thermal, structural, and dynamic properties which are compared with the values obtained from the analytical function. Our results show that, at least for LJ‐type potentials, NNs can be trained to generate accurate PES to be used in molecular simulations. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007

Performance characteristics of asphalt materials based on molecular dynamics simulation – A review

Molecular dynamics simulations of ionic systems require the inclusion of long-range electrostatic forces. We propose an expression for the long-range electrostatic forces based on an analytical solution of the Poisson–Boltzmann equation outside a spherical cutoff, which can easily be implemented in molecular simulation programs. An analytical solution of the linearized Poisson–Boltzmann (PB) equation valid in a spherical region is obtained. From this general solution special expressions are derived for evaluating the electrostatic potential and its derivative at the origin of the sphere. These expressions have been implemented for molecular dynamics (MD) simulations, such that the surface of the cutoff sphere around a charged particle is identified with the spherical boundary of the Poisson–Boltzmann problem. The analytical solution of the Poisson–Boltzmann equation is valid for the cutoff sphere and can be used for calculating the reaction field forces on the central charge, assuming a uniform continuum of given ionic strength beyond the cutoff. MD simulations are performed for a periodic system consisting of 2127 SPC water molecules with 40 NaCl ions (1 molar). We compare the structural and dynamical results obtained from MD simulations in which the long range electrostatic interactions are treated differently; using a cutoff radius, using a cutoff radius and a Poisson–Boltzmann generalized reaction field force, and using the Ewald summation. Application of the Poisson–Boltzmann generalized reaction field gives a dramatic improvement of the structure of the solution compared to a simple cutoff treatment, at no extra computational cost.

Lignin, as a major waste from biofuel and paper industries, could be utilized as a modifier to enhance the relevant performance of bitumen. However, the effects of lignin on the thermodynamics properties and molecular structure of bitumen are rarely studied. Meanwhile, the potential modification mechanism of lignin modified bitumen is still unclear. Molecular dynamics (MD) simulation and laboratory experimental methods are combined to explore the influence of lignin on the thermodynamics characteristics, rheological properties as well as the molecular structure of bitumen. The lignin modified bitumen with different dosages of lignin (10, 20 and 30 wt%) were prepared. DSR results from a macroscale view reveal that lignin could significantly improve the modulus, elastic recovery and rutting resistance of bitumen, but it adversely affects the fatigue performance. Meanwhile, the MD simulation results from a microscale perspective show that lignin could increase the density, cohesive energy density, shear viscosity, modulus and adhesive strength of bitumen. However, the free volume, diffusion coefficient and self-healing ability of lignin modified bitumen are weakened with the increase of lignin dosage. The MD simulations results are consistent with the experimental data. Furthermore, the correlations between the microscale and macroscale properties of lignin modified bitumen indicate that the physical and rheological properties of bitumen both depend on the molecular structure dramatically. The findings of this research can provide insights for an in-depth understanding of the effect of lignin on bitumen.

A combined study of experimental and molecular dynamics (MD) simulation methods is presented for hindered phenol AO‐80/nitrile‐butadiene rubber/poly(vinyl chloride) (AO‐80/NBR/PVC) composites with different AO‐80 contents to establish the microstructure‐damping property relations. MD simulation found that the AO‐80/NBR/PVC composite (abbreviated as AO‐80/NBVC) with an AO‐80 content of 99 phr had the largest hydrogen bonds (H‐bonds) and highest binding energy, indicating a good compatibility between NBR and AO‐80 and good damping performance of AO‐80/NBVC composites. Experimental results from SEM, DSC, and DMA were in good agreement with the MD simulation results. The tensile test results showed that the AO‐80/NBVC composite with an AO‐80 content of 99 phr had high tensile strength because of the strong H‐bonds of the composites and the disintegration and reintegration of the H‐bonds. The MD simulation technique proves to be a promising tool for the design and prediction of high damping properties of advanced composites in a microscopic view.

The bacterial SecYEG translocon functions as a conserved protein-conducting channel. Conformational transitions of SecYEG allow protein translocation across the membrane without perturbation of membrane permeability. Here, we report the crystal structures of intact SecYEG at 2.7-Å resolution and of peptide-bound SecYEG at 3.6-Å resolution. The higher-resolution structure revealed that the cytoplasmic loop of SecG covers the hourglass-shaped channel, which was confirmed to also occur in the membrane by disulfide bond formation analysis and molecular dynamics simulation. The cytoplasmic loop may be involved in protein translocation. In addition, the previously unknown peptide-bound crystal structure of SecYEG implies that interactions between the cytoplasmic side of SecY and signal peptides are related to lateral gate opening at the first step of protein translocation. These SecYEG structures therefore provide a number of structural insights into the Sec machinery for further study.

Molecular dynamics simulation as a tool for prediction of the properties of TiO2 and TiO2:MoO3 based chemical gas sensors

Microscopic mechanism of enhancing shale oil recovery through CO2 flooding- insights from molecular dynamics simulations

Our recent studies revealed that none of the selected widely used force field parameters and molecular dynamics simulation techniques yield structural properties for the intrinsically disordered α-synuclein that are in agreement with various experiments via testing different force field parameters. Here, we extend our studies on the secondary structure properties of the disordered amyloid-β(1-40) peptide in aqueous solution. For these purposes, we conducted extensive replica exchange molecular dynamics simulations and obtained extensive molecular dynamics simulation trajectories from David E. Shaw group. Specifically, these molecular dynamics simulations were conducted using various force field parameters and obtained results are compared to our replica exchange molecular dynamics simulations and experiments. In this study, we calculated the secondary structure abundances and radius of gyration values for amyloid-β(1-40) that were simulated using varying force field parameter sets and different simulation techniques. In addition, the intrinsic disorder propensity, as well as sequence-based secondary structure predisposition of amyloid-β(1-40) and compared the findings with the results obtained from molecular simulations using various force field parameters and different simulation techniques. Our studies clearly show that the epitope region identification of amyloid-β(1-40) depends on the chosen simulation technique and chosen force field parameters. Based on comparison with experiments, we find that best computational results in agreement with experiments are obtained using the a99sb*-ildn, charmm36m, and a99sb-disp parameters for the amyloid-β(1-40) peptide in molecular dynamics simulations without parallel tempering or via replica exchange molecular dynamics simulations.