Simulation of Amorphous Nylon 6 Using SuSi,a Strategy Based on Generation–Relaxation Algorithms

Summary: The ability of SuSi to generate microstructures of polymers with hydrogen bonding interactions has been checked. This is a random procedure recently developed to localize independent minima. Calculations were performed on nylon 6, a large number of equilibrated and relaxed atomistic models, i.e. microstructures without torsional strain and atomic overlaps, being generated. Results indicated that the generation algorithm implemented in SuSi underestimates the amount of amide groups involved in hydrogen bonding interactions. This is an expected result since no specific criterion was introduced in it to facilitate the formation of specific interactions. Several modifications have been introduced in the generation algorithm to overcome this limitation. The changes induced by these modifications in the generated microstructures are discussed.

A new computational strategy denoted SuSi generates atomistic models of hydrogen bond forming polymers with very reliable results.     

Coarse-graining: a procedure to generate equilibrated and relaxed models of amorphous polymers

We present a coarse-graining procedure to construct models of amorphous polymers. The method, which was applied to polyethylene, is based on a generation-relaxation strategy previously developed to provide independent atomistic microstructures. The coarse-graining was performed by assigning positions to mesoscopic particles denoted blobs, which represent groups of atoms, through distance, angle and dihedral distribution functions. The interaction energy between pairs of blobs was evaluated through a soft potential, whose parameters were derived from atomistic models. Three levels of coarse-graining that differ in the number of atoms included in the blob have been considered. The structural and energy-related properties calculated using the coarse-grained models developed in this study are in good agreement with those obtained using atomistic simulations.     

Structural aspects of deformation of amorphous polymers

Experimental and theoretical data on the inelastic deformation of amorphous glassy polymers were analyzed. The decisive role of direct structural methods in determination of the deformation mechanism of glassy polymers was established. A new mechanism of deformation and thermally stimulated recovery of strained glassy polymers was considered on the basis of structural data analysis.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 1–6, January, 2005.     

Relationship between the α‐ and β‐relaxation processes in amorphous polymers: Insight from atomistic molecular dynamics simulations of 1,4‐polybutadiene melts and blends

Amorphous polymers exhibit a primary (glass, or α‐) relaxation process and a low‐temperature relaxation process associated with polymer backbone motion usually referred to as the β‐relaxation process. The latter process can be observed below the glass transition temperature of the polymer and usually merges with the α‐relaxation process at temperatures somewhat above the glass transition temperature. While it is widely held that both the α‐relaxation and β‐relaxation processes are engendered by localized (segmental) motions of the polymer backbone, and that there is a strong mechanistic connection between them, the molecular mechanisms of the α‐relaxation and β‐relaxation processes in amorphous polymers are not well understood. Recently, atomistic molecular dynamics simulations of melts and blends of 1,4‐polybutadiene have provided insight into the relationship between the α‐ and β‐relaxation processes in glass‐forming polymers and an improved understanding of their molecular origins. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 627–643, 2007     

Atomic mobility in strained glassy polymers: The role of fold catastrophes on the potential energy surface

Deformation is known to enhance the atomic mobility in disordered systems such as polymer materials. To elucidate the origin of this phenomenon, we carry out two types of simulations: molecular dynamics (MD) simulations, which determine the atomic trajectories at finite temperature, and quasi-static simulations, which determine the atomic trajectories in the limit of zero temperature (and in the limit of zero shear rate). The quasi-static simulations show discontinuous changes in properties, such as system energy and atomic mobility. We use a normal mode analysis to show that these discontinuous changes arise from fold catastrophes of the potential energy landscape, in which energy minima flatten out and the heights of energy barriers decrease to zero; this was demonstrated by normal mode frequencies following a power law with an exponent of 0.5 as the discontinuous change is approached. After the fold catastrophe, the system relaxes to a different energy minimum, giving rise to atomic displacements. These fold catastrophes are the only mechanism for diffusive atomic displacements in the quasi-static simulations, where there is no thermal energy. We compared the mean-squared displacements as a function of strain from the quasi-static simulations to those from MD simulations (which do include thermal effects)—the similarity of the values of the mean-squared displacements in these two types of simulations demonstrates that the fold catastrophes underlie the enhanced dynamics in strained polymer systems even at finite temperature. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012     

Prediction of solvent diffusion coefficient in amorphous polymers based on an equation‐of‐state

This study develops a modified free‐volume model to predict solvent diffusion coefficients in amorphous polymers by combining the Vrentas–Duda model with the Simha–Somcynsky (S‐S) equation‐of‐state (EOS), and all the original parameters can be used in the modified model. The free volume of the polymer is estimated from the S‐S EOS together with the Williams‐Landel‐Ferry fractional free volume, and the complex process of determining polymer free‐volume parameters in the Vrentas–Duda model and measuring polymer viscoelasticity can be avoided. Moreover, the modified model includes the influence of not only temperature but also pressure on solvent diffusivity. Three common polymers and four solvents are employed to demonstrate the predictions of the modified model. The calculation results are generally consistent with the experimental values. It is reasonable to expect that the modified free‐volume model will become a useful tool in polymer process development. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1000–1009, 2006     

Synthesis of bistriphenylamine‐ and benzodithiophene‐based random conjugated polymers for organic photovoltaic applications

In this study, donor–acceptor random polymers containing benzotriazole acceptor and bistriphenylamine and benzodithiophene donors, P1 and P2 , were successfully synthesized by Stille coupling polymerization. The effect of bistriphenylamine moiety and thiophene π‐conjugated linker on electrochemical, spectroelectrochemical, and optical behaviors of the polymers were investigated. Optoelectronic properties and photovoltaic performance of the polymers were examined under the illumination of AM 1.5G, 100 mW cm^?2. The polymers were characterized by cyclic voltammetry, UV‐Vis‐NIR absorption spectroscopy, gel permeation chromatography. HOMO/LUMO energy levels of P1 and P2 were calculated as ?5.47 eV/–3.41 eV and ?5.43 eV/–3.27 eV, respectively. Bulk heterojunction type solar cells were constructed using blends of the polymers (donor) and [6,6]‐phenyl C₇₁ butyric acid methyl ester (PC₇₁BM) (acceptor). Photovoltaic studies showed that the highest power conversion efficiency of these photovoltaic devices were recorded as 3.50% with open circuit voltage; 0.79 V, short circuit current; 9.45 mA cm^?2, fill factor; 0.53 for P1 :PC₇₁BM (1:2, w/w) in 3% o‐dichlorobenzene (o‐DCB) solution and 3.15% with open circuit voltage; 0.75 V, short circuit current; 8.59 mA cm^?2, fill factor; 0.49 for P2 :PC₇₁BM (1:2, w/w) in 2% chlorobenzene (CB) solution. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55 , 3705–3715     

The effect of ionic electrolytes on hydrolytic degradation of biodegradable polymers: Mechanical and thermodynamic properties and molecular modeling

The purpose of this study was to examine the effect of electrolytes on the hydrolytic degradation of synthetic biodegradable polymers and fibers. Both Polyglycolic acid (PGA) and poly(glycolide–lactide) copolymer (PGL) were used for the study. Four different electrolytes were used: NaCl, LiCl, MgCl₂, and ZnCl₂. The electrolyte effect was evaluated in terms of the change in tensile properties, water uptake, and surface morphology of the polymers and fibers. It was found that the NaCl and MgCl₂ solutions significantly retarded the hydrolytic degradation of both PGA and PGL as evidenced in the prolonged retention of tensile breaking strength of these fibers when compared to deionized water control. Increasing the concentration of the electrolyte retarded the hydrolytic degradation rate further. These mechanical property data agreed well with the rate and amount of water uptake of PGA and could be correlated with the chemical potential difference of water between the electrolyte solution and pure water. The effect of electrolyte was further analyzed by theoretical calculation. Semiemperical molecular orbital calculations indicated that hard cations like Mg, Li, and Zn strongly coordinated to the polar sites of the polymer chain segments (? C?O) and severely disrupted their solvation spheres. Such a disruption was reflected in the smaller amount and slower rate of water uptake by PGA, and thus a slower rate of hydrolytic degradation as evident in the retention of tensile breaking strength. © 1993 John Wiley & Sons, Inc.     

Synthesis and photovoltaic properties of amorphous polymers based on dithienylbenzothiadiazole‐triphenylamine with hexyl side chains on different positions of thienyl groups

We synthesized and characterized three new amorphous dithienylbenzothiadiazole (TBT)‐triphenylamine (TPA) polymers for application in bulk‐heterojunction (BHJ) organic photovoltaic (OPV) cells. Poly(3HTBT‐TPA) has hexyl side chains on the thienyl groups (pointing toward the benzothiadiazole (BTD) unit), and poly(4HTBT‐TPA) has hexyl side chains on the thienyl groups (pointing outward from the BTD unit). The incident photon to current conversion efficiencies (IPCEs) in the region from 550 to 650 nm for the OPV cells prepared using poly(4HTBT‐TPA) were higher than those for the OPV cells prepared using poly(3HTBT‐TPA) because the absorption spectrum for the poly(4HTBT‐TPA) has a slightly red‐shifted absorption edge. We also demonstrated that the poly(4HTBT‐TPA)‐based OPV performance is independent of the fabrication process, so using an amorphous film to fabricate BHJ OPV cells offers great advantages over using a polycrystalline film in terms of the high reproducibility of the OPV performance. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 2536–2544     

The mechanism and a slip model for the initial plastic deformation of amorphous polyethylene under uniaxial tension

The mechanical behaviors of a polyethylene (PE) bulk consisting of amorphous molecular chains under uniaxial tension have been explored using molecular simulations. The stress–strain relationship and the plastic deformations of the PE bulk have been analyzed. Two deformation stages were found in the stress–strain curve, the elastic stage with a straight linear part of the curve and the plastic stage with a flat sawtooth‐like part. The Young's modulus calculated from the elastic part is in good agreement with experimental results. Some key parameters such as the energy variations in different terms reveal that the interchain slip should be chiefly responsible for the initial plastic deformations of amorphous PE under uniaxial tension. In order to address how this slip influences the plastic deformations, the mechanical details of a single chain have been elucidated when it was pulled out from two PE clusters consisting of regular and amorphous chains, respectively. The interchain slip, found as the basic movement style, is responsible for the movement of the stretched chain. Both the critical slip force and the critical slip length have been found in these two cases. For the straight chain pulled out from the cluster with regular chains, the critical slip force is about 1.81 nN and the critical slip length is about 40 polymerization degrees. While for the chain in the amorphous cluster, the critical force is about 0.86 nN and the critical length is almost the same. Based on the simulation results, a meso slip model has been deduced to explain the behaviors of the amorphous PE bulk under uniaxial tension. With reference to the slip model of single crystals and polycrystals a constitutive relation was obtained by considering the Young's modulus, the equivalent slip stress and the average orientation parameters of each chain. The comparison of the results from the constitutive relation and the simulations proves that this model does well in predicting the mechanical behaviors of amorphous PE under uniaxial tension in general. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 986–998     

Inclusion of the effects of polydispersity and volatility on the random chain scission statistical analysis for polymer degradation

The statistical product distribution for a linear polydisperse polymer of finite molecular weight was included into the statistical analysis for a system undergoing random chain scission showing the effect of volatilization of species other than monomer. Two sets of equations were derived. One set is for the nonvolatile fraction; the other is for the volatile fraction. Within each set there are three equations, one for the number of polymer molecules, the second for the molar (or number) fraction, and the third for the weight fraction of polymer molecules containing a specific number of repeat units. As degradation proceeds the polydispersity index should converge to a value of 1 rather than 2, which has been reported previously. The expected effects of polydispersity, number‐average degree of polymerization, and volatility were treated individually, and we determined that the molecular weight of a polymer has no theoretical influence on the product distribution. As for the effect of volatility, we determined that only the volatile product distribution would change. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 3690–3696, 2000     

Three Cd(II) coordination polymers based on a pyridyldicarboxylate: effect of coordinated water

Abstract

By systematic change of the solvothermal synthesis, three new coordination polymers, [Cd(L)?(H₂O)]?2H₂O (1), [Cd(L)?(H₂O)]?H₂O (2), and [Cd(L)] (3), have been synthesized based on a tritopic ligand 4-(pyridin-3-yl)isophthalic acid (H₂L). Compounds 1 and 2 show very similar two-dimensional (2D) bilayers further linked by interlayer hydrogen bonds into three-dimensional (3D) supramolecular structures, while 3 displays a 3D structure constructed form one-dimensional (1D) Cd-carboxyl chains. Notably, 1 and 2 have a pair of unusual isomers with the opposite orientation of coordinated H₂O on the metal centers, leading to different hydrogen bonding interactions. Thermal stabilities and solid-state photoluminescences for 1–3 were also investigated.     

Scaling and structural properties of a polymer in a simple solvent: A study based on integral equations

We present a statistical mechanical theory for polymer–solvent systems based on integral equations derived from the polymer Kirkwood hierarchy. Integral equations for pair monomer–monomer, monomer–solvent, and solvent–solvent correlation functions yield polymer–solvent distribution, chain conformation in three dimensions, and scaling properties associated with polymer swell and collapse in athermal, good, and poor solvents. Variation of polymer properties with solvent density and solvent quality is evaluated for chains having up to 100 bonds. In good solvents, the scaling exponent v has a constant value of about 0.61 at different solvent densities computed. For the athermal solvent case, the gyration radius and scaling exponent decrease with solvent density. In a poor solvent, the chain size scales as N^v with the value of the exponent being about 0.3, compared with the mean field value of ⅓. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36: 3025–3033, 1998     

Iterative method for finding the low‐energy conformations based on the concept of molecular volumes

The recently proposed overlapping spheres (OS) method (Raos, N. Croat Chem Acta 1999, 72, 727) finds low‐energy conformations by minimizing the repulsion potential dependent on the free molecular volume inside the sphere with radius R_v. The sphere is situated at the geometrical center of the molecule or at the center of a molecular segment. The method was checked on branched alkanes and cyclic molecules (1,4‐diethylcyclohexane and copper(II) monochelates with N‐alkylated amino acids), yielding in all cases stable conformations with usually lower conformational energy than the “seed” conformations. The simple rules for segmentation of a molecule, based mostly on the topological considerations, were derived from the results of successfull optimizations. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1353–1360, 2000     

Mechanical and barrier properties of ternary nanocomposite films based on polycarbonate/amorphous polyamide blends modified with a nanoclay

Ternary polycarbonate (PC)/amorphous polyamide–nanoclay (naPA) nanocomposite (PC/naPA) films were obtained by melt mixing and drawing, and the effects of the naPA content and the draw ratio (DR) on the structure, morphology and mechanical and barrier properties were studied. Despite the presence of nanoclay, the films exhibited a negligible roughness and the excellent optical properties of PC and amorphous polyamide (aPA). The dispersed naPA phase was pure and small, indicating compatibility. The naPA did not hinder the drawing ability of PC. At low DRs the dispersed phase was elongated and oriented along the machine direction (extrusion flow direction), but at high DRs, it fibrillated due to the higher non‐isothermal elongational flow induced by drawing. The laminar structure of the nanoclay allowed the films to be reinforced both in the machine and the transverse directions. The oxygen permeability of PC was reduced by 42% in the nanocomposite with 25% of naPA, and dropped further with the DR, which is attributed to the increased tortuosity of the oxygen path induced by fibrillation. Copyright © 2015 John Wiley & Sons, Ltd.     

Sulphur-containing polymers: Synthesis and thermal properties of novel polyesters based on dithiotriethylene glycol

Poly(dithiotriethylene terephthalate) (PSSTET), poly(dithiotriethylene adipate) (PSSTEA), poly(triethylene terephthalate) (PTET) and poly(triethylene adipate) (PTEA), these two last for comparison, were synthesized and characterized in terms of chemical structure and molecular weight. The thermal behaviour was examined by thermogravimetric analysis and differential scanning calorimetry. All the polymers showed a good thermal stability, even though lower for the sulphur-containing polyesters. At room temperature they appeared as semicrystalline materials, except PTEA, which was an oil; the effect of substitution of ether oxygen atoms with sulphur ones was found to be a lowering in the T_g value, an increment of the melting temperature and an increase of the crystallization rate. The results were explained as due to the presence of flexible C-S-C bonds in the polymeric chain. Lastly, the absence of a rigid-amorphous phase was evidenced in PSSTET and PTET.     

Q-fit: a probabilistic method for docking molecular fragments by sampling low energy conformational space

A new method is presented that docks molecular fragments to a rigid protein receptor. It uses a probabilistic procedure based on statistical thermodynamic principles to place ligand atom triplets at the lowest energy sites. The probabilistic method ranks receptor binding modes so that the lowest energy ones are sampled first. This allows constraints to be introduced to limit the depth of the search leading to a computationally efficient method of sampling low energy conformational space. This is combined with energy minimization of the initial fragment placement to arrive at a low energy conformation for the molecular fragment. Two different search methods are tested involving (i) geometric hashing and (ii) pose clustering methods. Ten molecular fragments were docked that have commonly been used to test docking methods. The success rate was 8/10 and 10/10 for generating a close solution ranked first using the two different sampling procedures. In general, all five of the top ranked solutions reproduce the observed binding mode, which increases confidence in the predictions. A set of ten molecular fragments that have previously been identified as problematic were docked. Success was achieved in 3/10 and 4/10 using the two different methods. Again there is a high level of agreement between the two methods and again in the successful cases the top ranked solutions are correct whilst in the case of the failures none are. The geometric hashing and pose clustering methods are fast averaging 13 and 11 s per placement respectively using conservative parameters. The results are very encouraging and will facilitate the process of finding novel small molecule lead compounds by virtual screening of chemical databases.     

Synthesis and characterization of porphyrin‐based D‐π‐A conjugated polymers for polymer solar cells

Two novel porphyrin‐based D‐A conjugated copolymers, PFTTQP and PBDTTTQP , consisting of accepting quinoxalino[2,3‐b′]porphyrin unit and donating fluorene or benzo[1,2‐b:4,5‐b′]dithiophene unit, were synthesized, respectively via a Pd‐catalyzed Stille‐coupling method. The quinoxalino[2,3‐b′]porphyrin, an edge‐fused porphyrin monomer, was used as a building block of D‐A copolymers, rather than the simple porphyrin unit in conventional porphyrin‐based photovoltaic polymers reported in literature, to enhance the coplanarity and to extend the π‐conjugated system of polymer main chains, and consequently to facilitate the intramolecular charge transfer (ICT). The thermal stability, optical, and electrochemical properties as well as the photovoltaic characteristics of the two polymers were systematically investigated. Both the polymers showed high hole mobility, reaching 4.3 × 10^?4 cm² V^?1 s^?1 for PFTTQP and 2.0 × 10^?4 cm² V^?1 s^?1 for PBDTTTQP . Polymer solar cells (PSCs) made from PFTTQP and PBDTTTQP demonstrated power conversion efficiencies (PCEs) of 2.39% and 1.53%, both of which are among the highest PCE values in the PSCs based on porphyrin‐based conjugated polymers. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013     

Biomacromolecule template‐based molecularly imprinted polymers with an emphasis on their synthesis strategies: a review

Molecular imprinting is an efficient tool for generating synthetic acceptors with specific recognition sites, which are mimed from template structures via polymerization. The final products of this strategy lead to high‐performance polymers with active recognition sites for a range of various applications in terms of extraction and separation, characterization and recognition, biomedicine, biosensors, and drug delivery. Molecular imprinting of biomacromolecules synthesizes a series of matrices that may be referred to as biomolecularly imprinted polymers (BMIPs). In this review article, an overview of different methods for fabricating BMIPs with an emphasis on novel polymerization schemes along with potential challenges is discussed. Additionally, selected applications of BMIPs will be briefly highlighted derived from the latest research papers. Copyright © 2016 John Wiley & Sons, Ltd.