Molecular dynamics simulation of liquid water and ice nanoclusters using a new effective HFD‐like model

We have determined a new two‐body interaction potential of water by the inversion of viscosity collision integrals of water vapor and fitted to achieve the Hartree–fock dispersion‐like (HFD‐like) potential function. The calculated two‐body potential generates the thermal conductivity, viscosity, and self‐diffusion coefficient of water vapor in an excellent accordance with experimental data at wide temperature ranges. We have also used a new many‐body potential as a function of temperature and density with the HFD‐like pair‐potential of water to improve the two‐body properties better than the SPC, SPC/E, TIP3P, and TIP4P models. We have also used the new corrected potential to simulate the configurational energy and the melting temperatures of the (H₂O)₅₀₀, (H₂O)₈₆₄, (H₂O)₂₀₄₈, and (H₂O)₆₉₁₂ ice nanoclusters in good agreement with the previous simulation data using the TIP4P model. The extrapolated melting point at the bulk limit is also in better agreement with the experimental bulk data. The self‐diffusion coefficients for the ice nanoclusters also simulated at different temperatures. © 2017 Wiley Periodicals, Inc.     

Correlations and Fluctuations of Charged Colloids as Determined by Anomalous Small‐Angle X‐Ray Scattering

Summary: We performed molecular dynamics simulation of a charged colloidal particle with explicit counterions. Our work provides a direct comparison between simulations and ASAXS‐experiments, offering insight into the counterion distribution of charged colloidal suspensions. We give a detailed constitution of the appearing scattering terms with their physical meaning. It is shown that the cross‐correlation between a macroion and its counterions gives the meanfield approximation of the counterion density even if the counterion system is highly fluctuating. Furthermore, it is shown that cross‐correlations can be negative due to oscillations of the density amplitudes of the macroion and counterions and, therefore, must be distinguished from other scattering contributions. These oscillations become more pronounced if the counterions exhibit a fixed shape and if the size of the macroion and that of the counterion system are different.

Simulation sanpshot of a charged colloid (big central sphere) with counterions (small spheres).     

Algorithms for GPU‐based molecular dynamics simulations of complex fluids: Applications to water,mixtures, and liquid crystals

A custom code for molecular dynamics simulations has been designed to run on CUDA‐enabled NVIDIA graphics processing units (GPUs). The double‐precision code simulates multicomponent fluids, with intramolecular and intermolecular forces, coarse‐grained and atomistic models, holonomic constraints, Nosé–Hoover thermostats, and the generation of distribution functions. Algorithms to compute Lennard‐Jones and Gay‐Berne interactions, and the electrostatic force using Ewald summations, are discussed. A neighbor list is introduced to improve scaling with respect to system size. Three test systems are examined: SPC/E water; an n‐hexane/2‐propanol mixture; and a liquid crystal mesogen, 2‐(4‐butyloxyphenyl)‐5‐octyloxypyrimidine. Code performance is analyzed for each system. With one GPU, a 33–119 fold increase in performance is achieved compared with the serial code while the use of two GPUs leads to a 69–287 fold improvement and three GPUs yield a 101–377 fold speedup. © 2015 Wiley Periodicals, Inc.     

Coarse‐grained A‐graft‐B model of poly(lactic acid) for molecular dynamics simulations

A mesoscopic model of poly(lactic acid) is developed where the polymer is represented as an A‐graft‐B chain with monomer units consisting of two covalently connected beads. A coarse‐graining algorithm is proposed to convert an atomistic model of PLA into a coarse‐grained one. The developed model is based on atomistic simulations of oligolactides to take into account terminal groups correctly. It was used for coarse‐grained simulations of polylactide. Gyration radii and end to end distances of polymer chains as well as the density of the polymer melt are shown to be in a good agreement with those obtained from atomistic simulations. The thermal expansion coefficients of the OLA melts calculated using the coarse‐grained model are in reasonable agreement with those obtained from all‐atom molecular dynamics. The model provides a 17‐fold speedup compared with atomistic calculations. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 604–612     

Determination of total phthalates in edible oils by high‐performance liquid chromatography coupled with photodiode array detection

The previously reported procedure for the determination of the total phthalate in fatty food involved the extraction of phthalates using chloroform/methanol followed by the removal of the solvents before alkaline hydrolysis requiring 20 h and derivatization of phthalic acid. In this study, a phase‐transfer catalyst (tetrabutylammonium chloride) was used in the liquid–liquid heterogeneous hydrolysis of phthalates in oil matrix shortening the reaction time to within 25 min. The resulting phthalic acid in the hydrolysate was extracted by a novel molecular complex based dispersive liquid–liquid microextraction method coupled with back‐extraction before high‐performance liquid chromatography coupled with photodiode array detection. Under the optimal experimental conditions, the linearity of the method was in the range of 0.5–12 nmol/g with the correlation coefficients (r) >0.997. The detection limit (S/N = 3) was 0.11 nmol/g. Intraday and interday repeatability values expressed as relative standard deviation were 3.9 and 7.1%, respectively. The recovery rates ranged from 82.4 to 99.0%. The developed method was successfully applied for the analysis of total phthalate in seven edible oils.     

Short‐time elasticity of polymer melts: Tobolsky conjecture and heterogeneous local stiffness

An extended molecular‐dynamics study of the short‐time “glassy” elasticity exhibited by a polymer melt of linear fully‐flexible chains above the glass transition is presented. The focus is on the infinite‐frequency shear modulus G_∞ manifested in the picosecond time scale and the relaxed plateau G_p reached at later times and terminated by the structural relaxation. The local stiffness of the interactions with the first neighbors of each monomer exhibits marked distribution with average value given by G_∞. In particular, the neighborhood of the end monomers of each chain are softer than the one of the inner monomers, so that G_∞ increases with the chain length. G_p is not affected by the chain length and is largely set by the nonbonding interactions, thus confirming for polymer melts the conjecture formulated by Tobolsky for glassy polymers. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 1401–1407     

Computational design of protein–ligand binding: Modifying the specificity of asparaginyl‐tRNA synthetase

A method for computational design of protein–ligand interactions is implemented and tested on the asparaginyl‐ and aspartyl‐tRNA synthetase enzymes (AsnRS, AspRS). The substrate specificity of these enzymes is crucial for the accurate translation of the genetic code. The method relies on a molecular mechanics energy function and a simple, continuum electrostatic, implicit solvent model. As test calculations, we first compute AspRS‐substrate binding free energy changes due to nine point mutations, for which experimental data are available; we also perform large‐scale redesign of the entire active site of each enzyme (40 amino acids) and compare to experimental sequences. We then apply the method to engineer an increased binding of aspartyl‐adenylate (AspAMP) into AsnRS. Mutants are obtained using several directed evolution protocols, where four or five amino acid positions in the active site are randomized. Promising mutants are subjected to molecular dynamics simulations; Poisson‐Boltzmann calculations provide an estimate of the corresponding, AspAMP, binding free energy changes, relative to the native AsnRS. Several of the mutants are predicted to have an inverted binding specificity, preferring to bind AspAMP rather than the natural substrate, AsnAMP. The computed binding affinities are significantly weaker than the native, AsnRS:AsnAMP affinity, and in most cases, the active site structure is significantly changed, compared to the native complex. This almost certainly precludes catalytic activity. One of the designed sequences has a higher affinity and more native‐like structure and may represent a valid candidate for Asp activity. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Prediction of viscoelastic properties with coarse‐grained molecular dynamics and experimental validation for a benchmark polyurea system

To explore the relationship between microscopic structure and viscoelastic properties of polyurea, a coarse‐grained (CG) model is developed by a structure matching method and validated against experiments conducted on a controlled, benchmark material. Using the Green‐Kubo method, the relaxation function is computed from the autocorrelation of the stress tensor, sampled over equilibrium MD simulations, and mapped to a real time scale established by matching self‐diffusion rates of atomistic and CG models. Master curves computed from the predicted stress relaxation function are then compared with dynamic mechanical analysis experiments mapped to a wide frequency range by time–temperature superposition, as well as measurements of ultrasonic shear wave propagation. Computational simulations from monodisperse and polydisperse configurations, representative of the benchmark polyurea, show excellent agreement with the experimental measurements over a multidecade range of loading frequency. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 797–810     

Influence of molecular weight on the short‐channel effect in polymer‐based field‐effect transistors

In this study, we demonstrate how the intrinsic properties of a polymer can influence the electrical characteristics of organic field‐effect transistors (OFETs). OFETs fabricated with three batches of poly[2‐methoxy,5‐(3′,7′‐dimethyl‐octyloxy)]‐p‐phenylene vinylene (MDMO‐PPV) were investigated. The properties of the polymers were initially investigated using Fourier transform infrared spectroscopy (FTIR), impedance spectroscopy (IS), gel permeation chromotography (GPC), and cyclic voltammetry (CV), respectively. The structure and purity of the polymer batches were found to be very comparable, but the molecular weight (M_n and M_w) and polydispersity (PDI = M_w/M_n), varied between the samples and the HOMO and LUMO levels of the polymers were found to depend on the molecular weight properties. OFETs were then fabricated with the polymers and electrically characterized. It was observed that the channel current and the field‐effect mobility increase with increasing polymer molecular weight. The output characteristics of the transistors, on the other hand, were found to depend on the PDI of the polymer. Saturation of the channel current occurs at higher source–drain voltages and short‐channel behavior was observed to start at longer channel lengths for polymers with a higher PDI. This behavior is observed to be thickness dependent, and the short‐channel behavior was more pronounced for thicker MDMO‐PPV films. These results are explained in terms of influences of chain packing and ordering and high bulk currents on the FET output and transistor parameters. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 50: 117–124, 2012     

Cooperative Molecular Motion within a Self‐Assembled Liquid‐Crystalline Molecular Wire: The Case of a TEG‐Substituted Perylenediimide Disc

Always on the move : Molecular dynamics of perylene cores in columnar structures influences the processability and self‐healing of these materials. A combination of X‐ray scattering and advanced solid‐state NMR methods show that these systems have restricted angular mobility of the cores even in the frozen phase, and a cooperative spiral type of motion in the liquid crystalline phase (see picture).

     

Dynamic mechanical and dielectrical properties of poly(vinyl alcohol) and poly(vinyl alcohol)‐based nanocomposites

In this article we report on the investigation of the dynamics of poly(vinyl alcohol) (PVA) and PVA‐based composite films by means of dielectric spectroscopy and dynamic mechanical thermal analysis. Once the characterization of pure PVA was done, we studied the effect of a nanostructured magnetic filler (nanosized CoFe₂O₄ particles homogeneously dispersed within a sulfonated polystyrene matrix) on the dynamics of PVA. Our results suggest that the α‐relaxation process, corresponding to the glass transition of PVA, is affected by the filler. The glass‐transition temperature of PVA increases with filler content up to compositions of around 10 wt %, probably as a result of polymer–filler interactions that reduce the polymer chain mobility. For filler contents higher than 10 wt %, the glass‐transition temperature of PVA decreases as a result of the absorption of water that causes a plasticizing effect. The β‐ and γ‐relaxation processes of PVA are not affected by the filler as stated from both dynamic mechanical thermal analysis and dielectric spectroscopy. Nevertheless, both relaxation processes are greatly affected by the moisture content. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 1968–1975, 2001     

Predictors of Cavitation in Glassy Polymers under Tensile Strain: A Coarse‐Grained Molecular Dynamics Investigation

The nucleation of cavities in a homogeneous polymer under tensile strain is studied in a coarse‐grained MD simulation. To establish a causal relation between local microstructure and the onset of cavitation, a detailed analysis of some local properties is presented. In contrast to common assumptions, the nucleation of a cavity is neither correlated to a local loss of density nor to stress at the atomic scale or the chain‐end density in the nondeformed state. Instead, a cavity in glassy polymers nucleates in regions that display a low bulk elastic modulus. Even if the localization of a cavity is not directly predictable from the initial configuration, the elastically weak zones identified in the initial state emerge as favorite spots for cavity formation.

     

Evaluation of matrix effect in one‐dimensional and comprehensive two‐dimensional liquid chromatography for the determination of the phenolic fraction in extra virgin olive oils

Olea europaea, meaning “European olive,” is a small tree belonging to the family Oleaceae, occurring in the Mediterranean Basin. Olive oil is an essential component of a balanced diet because of its nutritional value. Among micronutrients, phenolic compounds did show important beneficial effects for human health. The majority of the research studies on the phenol content are carried out by liquid chromatography combined to photodiode array and/or mass spectrometry detection; however, because of matrix complexity, one‐dimensional liquid chromatography cannot be sometimes sufficient to obtain rewarding separations, requiring more advanced analytical techniques. In this work, comprehensive two‐dimensional liquid chromatography, incorporating RP‐Amide and C18 stationary phases, in the first and second dimension, respectively, both under reversed phase conditions, was investigated for the determination of the phenolic fraction in extra virgin olive oil samples. As far as detection is concerned, triple quadrupole mass spectrometry was employed under multi reaction monitoring mode offering superior selectivity and sensitivity. The reduction of matrix effects, when using comprehensive two‐dimensional liquid chromatography with respect to conventional one‐dimensional liquid chromatography, was assessed by comparing the slopes of calibration curves built from standard solutions and spiked olive oil samples.     

Pulling Polymers on Energetically Disordered Surfaces: Molecular Dynamics Tests of Linear and Non‐linear Response

Equilibrium and non‐equilibrium molecular dynamics simulations of flexible polymer chains absorbed on heterogeneous surfaces are presented. The surfaces are flat but energetically disordered, consisting of a random mixture of weakly and more strongly absorbing sites (94 and 6%, respectively). For comparison, the two corresponding homogeneous surfaces are also simulated. This apparently weak energetic disorder can produce significant changes of the chain statistics, equilibrium dynamics, and non‐equilibrium response to a horizontal pulling force. On the disordered surfaces, the polymer–surface effective friction coefficient becomes strongly force‐dependent, as the dominant mode of motion changes from localized stick–slip events to smooth and continuous sliding. This is strongly reminiscent of the Schallamach model of rubber friction and the Maier–Göritz picture of the Payne effect in filled elastomers.

     

Construction of three types of lanthanide complexes based on 3,4‐dimethylbenzoic acid and 5,5′‐dimethyl‐2,2′‐bipyridine: Syntheses,Structures, Thermodynamic properties,Luminescence, and Bacteriostatic activities

Three novel lanthanide complexes [Er (3,4‐DMBA)₃(5,5′‐DM‐2,2′‐bipy)(H₂O)] ( 1 ); [Tb₂ (3,4‐DMBA)₆(5,5′‐DM‐2,2′‐bipy)₂(H₂O)] ( 2 ); [Eu (3,4‐DMBA)₃(3,4‐DMHBA)(5,5′‐DM‐2,2′‐bipy)]₂ ( 3 ) (3,4‐DMHBA = 3,4‐dimethylbenzoic acid, 5,5′‐DM‐2,2′‐bipy =5,5′‐dimethyl‐2,2′‐bipyridine) were successfully synthesized via conventional solution method at room temperature and structurally characterized by single crystal diffraction. The structures of the complexes 1 – 3 were confirmed on the basis of elemental analysis, coordination titration analysis, IR and XRD. The molecular structures of complexes 2 and 3 are very particular: complex 2 has two same central metal ions but each metal ion has different coordination environment; in structure of the complex 3 , there are eight carboxylic acid ligands coordinated to the central metal ions, which have rarely been reported previously. The thermal decomposition mechanism of complexes 1 – 3 were investigated by the technology of simultaneous TG/DSC‐FTIR. The heat capacities of the complexes were recorded by means of DSC over the range of from 253.15 K to 345.15 K. The thermodynamic parameters, the smoothed values of heat capacities, enthalpy (H_T‐H_298.15K) and entropy (S_T‐S_298.15K) were also calculated. The bacteriostatic activities of the complexes were evaluated against Staphylococcus aureus, Escherichia coli and Candida albicans. What's more, the luminescence properties of complexes 2 and 3 were discussed, and their fluorescence lifetimes as well as the quantum yield of the Eu (III) were measured. To elucidate the energy transfer process of complexes 2 and 3, the energy levels of the relevant electronic states have been estimated.     

Effect of crosslinking polymer networks on the molecular reorientation and electro‐optical performance of in‐plane switching vertically aligned liquid crystal devices

The effects of crosslinking polymer networks (PNs) on the molecular reorientation and electro‐optical properties of vertically aligned (VA) liquid crystal (LC) devices are investigated by applying an in‐plane switching (IPS) electric field. Through the polymerization process, crosslinking PNs are developed on the substrate surface, effectively increasing the anchoring energy and governing the LC molecular reorientation. With its stronger anchoring effect, the PNs cell shows good light transmittance and excellent vertical alignment quality, as compared to the pure LC cell. Furthermore, the alignment transformation and transmittance bounce resulting from the transient process of LC molecular reorientation are eliminated when the cell is operated at high voltages. The rising‐time (t_r) and falling‐time (t_f) responses of the PNs cell are significantly improved, and around 36% improvement in the optical switching response is obtained. In addition, the dynamic gray‐level t_r and t_f responses of the PNs cell are enhanced by around 55% and 42%, respectively, at a low driving voltage (～12 V). This developed VA‐IPS LC/PNs cell benefits not only the LC molecular alignment but also the electro‐optical performance. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 1123–1130