Parameterization of electrostatic interactions for molecular dynamics simulations of heterocyclic polymers

The paper focuses on the problem of electrostatic interactions in molecular dynamics simulations of thermal properties of heterocyclic polymers. The study focuses on three thermoplastic polyimides synthesized on the basis of 1,3‐bis‐(3′,4‐dicarboxyphenoxy)benzene (dianhydride R) and three diamines: 4,4′‐bis‐(4″‐aminophenoxy) diphenylsulfone (diamine BAPS), 4,4′‐bis‐(4″‐aminophenoxy) biphenyl (diamine BAPB), and 4,4′‐bis‐(4''‐aminophenoxy) diphenyloxide (diamine BAPO). In the molecular dynamics simulations these polyimides were described by the Gromos53a5 force field. To parameterize the electrostatic interactions four methods of calculating the partial atomic charges were chosen: B3LYP/6–31G*(Mulliken), AM1(Mulliken), HF/6–31G*(Mulliken), and HF/6–31G*(ChelpG). As our parameterization is targeted to reproduce thermal properties of the thermoplastic polyimides, the choice of proper partial charges was finalized on a basis of the closest match between computational and experimental data for the thermal expansion coefficients of the polyimides below glass transition temperatures. Our finding clearly show that the best agreement with experimental data is achieved with the Mulliken partial atomic charges calculated by the Hartree‐Fock method with 6–31G* basis set. Furthermore, in addition to the thermal expansion coefficients this set of partial atomic charges predicts an experimentally observed relationship between glass transition temperatures of the three polyimides under study: . A mechanism behind the change in thermal properties upon the change in the chemical structure in considered polyimides may be related to an additional spatial ordering of sulfone groups due to dipole‐dipole interactions. Overall, the modified force‐field is proved to be suitable for accurate prediction of thermal properties of thermoplastic polyimides and can serve as a basis for building up atomistic theoretical models for describing other heterocyclic polymers in bulk. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 912–923     

Study of the molecular configuration and the dipole moment in fluorinated liquid crystals

We have investigated the relationship between the molecular configuration and dipole moment of some fluorinated liquid crystals (LCs). The geometries of the molecules were preliminarily optimized at empirical AM1 and then were further optimized at B3LYP/6‐31G(d) level. The dipole moment has been calculated. It is strongly influenced by the position and number of fluorine substituents in the benzene ring of the molecule. The polarizability, mean polarizabilities, and anisotropic polarizability of the phenylbicyclohexane (PBC) fluorine substituents are also given and discussed. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Influence of the electrostatic interactions on thermophysical properties of polyimides: Molecular‐dynamics simulations

Revealing the way of how modification of the chemical structure of a polymer affects its macroscopic physical properties offers an opportunity to develop novel polymer materials with pre‐defined characteristics. To address this problem two thermoplastic polyimides, ULTEM? and EXTEM?, were simulated with small difference in chemical structures of monomer units, namely, the phenyl ring in ULTEM? was replaced by the diphenylsulphone group in EXTEM?. It is shown that such a small modification results in a drastic difference of the thermal properties: the glass transition temperature of EXTEM? is higher than that of ULTEM?. Our molecular‐dynamics simulations clearly demonstrated that it is the electrostatic interactions that are responsible for the observed difference in thermal properties of ULTEM? and EXTEM?: large partial charges of the sulphone group in the EXTEM? lead to strong dipole–dipole intra‐ and intermolecular interactions and correspondingly to an elevated glass transition temperature. © 2014 Wiley Periodicals, Inc. J. Polym. Sci. Part B: Polym. Phys. 2014 , 52, 640–646     

Influence of molecular weight on some properties of liquid crystalline polyurethanes

This investigation extends our previous investigations of liquid crystalline polyurethanes prepared from 4,4′-bis(2-hydroxyethoxy)biphenyl (BHBP), 2,4-tolylene diisocyanate, and poly(oxytetramethylene)diols as the flexible spacers. The influence of molecular weight of investigated polyurethanes on their properties is discussed for two series with the same content of BHBP and different lengths of flexible spacers. The polyurethanes were investigated by means of DSC, polarizing microscopy, x-ray diffractometry, and IR spectroscopy. The molecular weight distribution was determined by GPC. Morphology was studied by the SALS method. The molecular weight of polyurethanes and the length of flexible spacer influence the phase transition temperature and the range of mesophase occurrence. © 1993 John Wiley & Sons, Inc.     

Phase transitions,optical, dielectric and viscoelastic properties of colloidal suspensions of BaTiO3 nanoparticles and cyanobiphenyl liquid crystals

We report experimental studies on the phase transitions and physical properties of colloidal suspensions of BaTiO₃ nanoparticles and two cyanobiphenyl liquid crystals (4-pentyl-4?-cyanobiphenyl and 4-octyl-4?-cyanobiphenyl). From the differential scanning calorimetric measurements, we show that the nanoparticles have antagonistic effect on the isotropic to nematic and nematic to smectic-A phase transitions. The birefringence, dielectric anisotropy and splay elastic constant remain almost unchanged, whereas the bend elastic constant and rotational viscosity decrease considerably. The experimental results are discussed based on the possible contribution of BaTiO₃ nanoparticles and free surfactant molecules in the suspensions.     

Non-covalent intermolecular interactions of colloidal nematic liquid crystals doped with graphene oxide

Graphene oxide (GO) was doped to eutectic uniaxial nematic liquid crystals (NLCs) (E_5CN7) with different percentages to improve the physiochemical properties of NLCs effectively. GO shifts the N-I phase transition temperature to higher values. It has been observed that increasing GO concentration up to 0.75% increases the N-I phase transition temperature substantially while further increase of GO concentration results in an inverse trend. The GO/E_5CN7 non-covalent interactions change the N-I phase transition. The contribution of several terms such as anchoring and polarisation effects on N-I phase transition was quantified as well. The results suggest that the size is an important contributor to GO and liquid crystal interaction. The results show that E_5CN7@GO composites may act as promising candidates to enhance the efficiency of room temperature devices.     

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.     

Determination of glass transition temperature of polyimides from atomistic molecular dynamics simulations and machine-learning algorithms

Glass transition temperature (T_g) plays an important role in controlling the mechanical and thermal properties of a polymer. Polyimides as an important category of engineering plastics have wide applications because of their superior heat resistance and mechanical strength. The capability of predicting T_g for a polyimide a priori is therefore highly desirable in order to expedite the design and discovery of new polyimide polymers with targeted properties and applications. Here we explore three different approaches to either compute T_g for a polyimide via all-atom molecular dynamics simulations or predict T_g via a mathematical model generated by using machine-learning algorithms to analyze existing data collected from the literature. Our simulations reveal that T_g can be determined from examining the diffusion coefficient of simple gas molecules in a polyimide as a function of temperature and the results are comparable to those derived from data on polymer density versus temperature and actually closer to the available experimental data. Furthermore, the predictive model of T_g derived with machine-learning algorithms can be used to estimate T_g successfully within an uncertainty of about 20 degrees, even for polyimides yet to be synthesized experimentally.     

Evaluation of phase state and rotational viscosity of fast response liquid crystals using a fully atomistic molecular dynamics

Rational design of liquid crystals (LCs) with excellent phase state and rotational viscosity has been a crucial technique for response speed improvement of LC wavefront corrector. A complete process for theoretically evaluating the phase state and rotational viscosity of fast response LCs using a fully atomistic molecular dynamics is reported. Predicted trends in molecular order, phase-transition temperature between metastable states and rotational viscosity show excellent agreement with experimental results. We also demonstrate that overestimation of the attraction both between and within molecules in the general Amber force field mainly leads to a systematic shift in the phase-transition temperature, rotational viscosity and figure-of-merit for fast response LCs. With further optimisations of intermolecular potential, simulation procedure and data processing, this fully atomistic simulation will be a useful evaluation method of response performance of LC materials.     

Mesophase study of pure and doped cyanobiphenyl liquid crystals with salen-type systems

Two salen Schiff base ligands derived from the condensation of ethylendiamine on salicylaldehyde and 5-chlorosalicylaldehyde, namely N,N′-bis(salicylidene)ethylene-diamine (L1) and N,N′-bis(5-chlorosalicylidene)ethylene-diamine (L2) as well as two of their iron(III) and nickel(II) complexes, were prepared and then used as doping agents of two thermotropic liquid crystals (LCs) of cyanobiphenyl type, namely 4-cyano-4′-n-pentyl-biphenyl (5CB) and 4-cyano-4′-n-octyl-biphenyl (8CB). The study of the mesophase of pure and doped LCs was carried out by UV–visible spectroscopy equipped with a heating compartment for precise temperature control, differential scanning calorimetry and polarised optical microscopy. The characteristic nematic/isotropic and smectic-A/nematic transition temperatures of 5CB- and 8CB-based systems were measured and then compared to those of the literature concerning pure 5CB and 8CB. Optical microscopy results revealed the existence of Schlieren and focal conic textures of the nematic and smectic states, respectively, both of pure and doped LCs. The homogeneity of the obtained guest–host systems was proven by the linear evolution of their transition temperatures as function of the solute concentration, with correlation factors close to unity.     

Collective and molecular dynamics in ferroelectric liquid crystals: from low molar to polymeric and elastomeric systems

Broadband dielectric spectroscopy delivers in the frequency range from 10 Hz to 10¹⁰ Hz two collective dielectric loss processes (soft and Goldstone modes) and one molecular relaxation (β-relaxation). The soft mode and Goldstone mode are assigned to the fluctuation of the amplitude and the phase of the helical superstructure. The β-relaxation corresponds to the libration (hindered rotation) of the mesogene around its long molecular axis. At the SmA–SmC^* phase transition this process does not split or broaden, and the temperature dependence of its relaxation rate does not show any deviation from an Arrhenius-like behavior. Its dielectric strength does not decline at the SmA–SmC^* phase transition. These experimental findings are in contrast to the common explanation of the origin of the saturation polarization (“induced spontaneous polarization”), which is based on the existence of a “free” rotation inside the SmA phase and its strong hindrance in the ferroelectric SmC^* phase. Furthermore, the high frequency results require a reformulation for the (generalized) Landau theory as applied to the SmA–SmC^* phase transition. In comparing low molar mass and polymeric (elastomeric) FLC, the collective and molecular dynamics are qualitatively similar, independent of the molecular architecture (e.g. side-chain, combined main- and side-chain or crosslinked systems).     

The effects of substituent size and molecular weight on the liquid crystalline properties of poly(2-alkyl-1,4-phenylene terephthalate)s

A series of low molecular weight, thermotropic poly(2-alkyl-1,4-phenylene terephthalate)s was prepared by the solution polycondensation reaction of terephthaloyl chloride and alkylhydroquinones containing n-alkyl substituents of increasing size from methyl to dodecyl. Samples of the low molecular weight polymers so obtained were also further polycondensed in the solid state to obtain high molecular weight polymers. The liquid crystalline phase behaviors and textures were determined, and the effects of polymer structure and molecular weight on these properties are discussed. All of the polymers obtained formed thermotropic, nematic mesophases, which were less stable for the lower molecular weight polymers, as expected, than were the mesophases formed by the higher molecular weight polymers. © 1994 John Wiley & Sons, Inc.     

Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations

We have used molecular dynamics simulations to study the physical properties of modified TIP3P water model included in the CHARMM program, using four different methods-the Ewald summation technique, and three different spherical truncation methods-for the treatment of the long-range interactions. Both the structure and dynamics of the liquid water model were affected by the methods used to truncate the long-range interactions. For some of the methods artificial structuring of the model liquid was observed around the cutoff radius. The model liquid properties were also affected by the commonly applied temperature control methods. Four different methods for controlling the temperature of the system were studied, and the effects of these methods on the bulk properties for liquid water were analyzed. The system size was also found to change the dynamics of the model liquid water. Two control simulations with the SPC/E water model were carried out. The self-diffusion coefficient (D), the radial distribution function (g(OO)), the distance dependent Kirkwood G-factor [G(k)(r)] and the intermolecular potential energy (E(pot)) were determined from the different trajectories and compared with the experimental data.     

Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

We present results of molecular dynamics simulations of fully hydrated DMPC bilayers performed on graphics processing units (GPUs) using current state-of-the-art non-polarizable force fields and a local GPU-enabled molecular dynamics code named FEN ZI. We treat the conditionally convergent electrostatic interaction energy exactly using the particle mesh Ewald method (PME) for solution of Poisson's Equation for the electrostatic potential under periodic boundary conditions. We discuss elements of our implementation of the PME algorithm on GPUs as well as pertinent performance issues. We proceed to show results of simulations of extended lipid bilayer systems using our program, FEN ZI. We performed simulations of DMPC bilayer systems consisting of 17,004, 68,484, and 273,936 atoms in explicit solvent. We present bilayer structural properties (atomic number densities, electron density profiles), deuterium order parameters (S(CD)), electrostatic properties (dipole potential, water dipole moments), and orientational properties of water. Predicted properties demonstrate excellent agreement with experiment and previous all-atom molecular dynamics simulations. We observe no statistically significant differences in calculated structural or electrostatic properties for different system sizes, suggesting the small bilayer simulations (less than 100 lipid molecules) provide equivalent representation of structural and electrostatic properties associated with significantly larger systems (over 1000 lipid molecules). We stress that the three system size representations will have differences in other properties such as surface capillary wave dynamics or surface tension related effects that are not probed in the current study. The latter properties are inherently dependent on system size. This contribution suggests the suitability of applying emerging GPU technologies to studies of an important class of biological environments, that of lipid bilayers and their associated integral membrane proteins. We envision that this technology will push the boundaries of fully atomic-resolution modeling of these biological systems, thus enabling unprecedented exploration of meso-scale phenomena (mechanisms, kinetics, energetics) with atomic detail at commodity hardware prices.     

Influence of branched chains on the mesomorphic properties of symmetrical and unsymmetrical triphenylene discotic liquid crystals

A series of novel symmetrical and unsymmetrical triphenylene‐based discotic liquid crystalline materials with one or six branched peripheral alkoxy chains have been prepared. These materials have been compared with analogous known symmetrical and unsymmetrical compounds to reveal a balance between steric and space‐filling effects of the peripheral branched chains, which significantly affects intermolecular forces of attraction and packing, and hence affects melting and isotropisation temperatures of the liquid crystalline materials. The desired result of reduction of melting points and enhancement of isotropisation temperatures has been accomplished by use of branched alkoxy chains in both symmetrical and unsymmetrical materials.     

Preorganised effects of a tetramesogenic supermolecule on supramolecular assembly in the liquid crystalline phases

After preparing a homologous series of tetrameric mesogenic compounds in which two U-shaped molecules were connected via a rigid benzene derivative or a flexible alkyl chain, we investigated their phase transition behaviour using optical microscopy, differential scanning calorimetry and X-ray diffraction analysis. The compounds possessing an alkyl spacer as the central group exhibited nematic and smectic A phases just as the corresponding U-shaped molecule did. The compound possessing a 1,2-benzene unit as the connecting group showed nematic and smectic A phases, although the compound possessing a 1,3-benzene unit exhibited only an anticlinic smectic C phase. Structure–property relations of the liquid crystalline tetramers are interpreted in terms of preorganised effects of the four mesogenic units.     

Comparison of the accuracy of periodic reaction field methods in molecular dynamics simulations of a model liquid crystal system

A periodic reaction field (PRF) method is a technique to estimate long‐range interactions. The method has the potential to effectively reduce the computational cost while maintaining adequate accuracy. We performed molecular dynamics (MD) simulations of a model liquid‐crystal system to assess the accuracy of some variations of the PRF method in low‐charge‐density systems. All the methods had adequate accuracy compared with the results of the particle mesh Ewald (PME) method, except for a few simulation conditions. Furthermore, in all of the simulation conditions, one of the PRF methods had the same accuracy as the PME method. © 2015 Wiley Periodicals, Inc.     

Calamitic liquid crystals of 1,2,3-triazole connected to azobenzene: synthesis,characterisation and anisotropic properties

Azobenzene-based calamitic liquid crystals, 4-((4-(4-methoxymethyl-1,2,3-triazol-1-yl)phenyl)diazenyl)phenylalkanoates have been isolated and their structures were characterised. The structure–property correlation with respect to the different alkanoyloxy terminal chain (–COOC_nH_2n+1 where n adopts odd numbers ranging from 3 to 15) has also been given attention in the present study. In this series, all compounds exhibit smectogenic properties. The lower homologues shows enantiotropic SmA phase as well as monotropic SmC phase. The higher homologues exhibit homeotropic alignment of smectic phases. These compounds possess very high anisotropic inclination in which the mesomorphic region covers nearly 80°C.