Chain-folded Structure Research Articles

Insights into the Phase Diagram of Pluronic L64 Using Coarse-Grained Molecular Dynamics Simulations.

We investigate the concentration-dependent phase diagram of pluronic L64 in aqueous media at 300 and 320 K using coarse-grained (CG) molecular dynamics (MD) simulations. The CG model is derived by adapting the Martini model for nonbonded interactions along with the Boltzmann inversion (BI) of bonded interactions from all-atom (AA) simulations. Our derived CG model successfully captures the experimentally observed micellar-, hexagonal-, lamellar-, and polymer-rich solution phase. The end-to-end distance reveals the conformational change from an open-chain structure in the micellar phase to a folded-chain structure in the lamellar phase, increasing the orientational order. An increase in temperature leads to expulsion of water molecules from the L64 moiety, suggesting an increase in L64 hydrophobicity. Thermodynamic analysis using the two-phase thermodynamics (2PT) method suggests the entropy of the system decreases with increasing L64 concentration and the decrease in free energy (F) with temperature is mainly driven by the entropic factor (-TS). Further, the increase in aggregation number at lower concentrations and self-assembly at very high concentrations is energetically driven, whereas the change from the micellar phase to the lamellar phase with increasing L64 concentration is entropically driven. Our model provides molecular insights into L64 phases which can be further explored to design functionality-based suprastructures for drug delivery and tissue engineering applications.

Enhanced ion transport behaviors in composite polymer electrolyte: the case of a looser chain folding structure

CPEs with smaller size of Al2O3 nano-particles leads to shorter spin-lattice relaxation time (T1) and longer transverse relaxation time (T2), implying a looser chain folding structure in CPEs, which provides more transport channels and conducting pathways for the Li-ions transportation.

Change of lamellar morphology upon polymorphic transition of form II to form I crystals in isotactic Polybutene-1 and its copolymer

Morphology and domain sizes in isotactic polybutene-1 homopolymer (iPB-1) and (butene-1)-ethylene random copolymer (iPB-1/C2) are studied by spin-diffusion time-domain 1H NMR and SAXS experiments. Lamellar thickness is smaller for iPB-1/C2 than for iPB-1 and decreases with decreasing crystallization temperature. iPB-1/C2 with form I’ crystals, which were directly formed upon crystallization from a heterogeneous melt, has typical for polyolefins lamellar morphology with the crystal-amorphous interface that separates crystal lamellae and interlamellar amorphous domains. Different lamellar structure is observed in iPB-1 and iPB-1/C2 with form I crystals which were obtained upon polymorphic phase transition from form II to form I crystals. The phase transition causes fragmentation of crystal lamellae into small blocks with a wide size distribution as was shown by the NMR method. Two types of the interface are present in these samples: the inner interface that separates crystal blocks within fragmented crystal lamellae, and the crystal-amorphous interface on the surface of fragmented lamellae. The molecular mechanism of polymorphic form II to form I phase transition is proposed. High chain mobility in form II crystals and chain folding structure on the lamellar surface play significant role at the initial and final stages of the restructuring of crystal lamellae during the phase transition, respectively.

Chain-folded lamellar structure and dynamics of the crystalline fraction of Bombyx mori silk fibroin and of (Ala-Gly-Ser-Gly-Ala-Gly)n model peptides

Solid-state NMR is a powerful analytical technique to determine the composite structure of Bombyx mori silk fibroin (SF). In our previous paper, we proposed a lamellar structure for Ala-Gly copolypeptides as a model of the crystalline fraction in Silk II. In this paper, the structure and dynamics of the crystalline fraction and of a better mimic of the crystalline fraction, (Ala-Gly-Ser-Gly-Ala-Gly)n (n = 2–5, 8), and 13C selectively labeled [3-13C]Ala-(AGSGAG)5 in Silk II forms, were studied using structural and dynamical analyses of the Ala Cβ peaks in 13C cross polarization/ magic angle spinning NMR and 13C solid-state spin-lattice relaxation time (T1) measurements, respectively. Like Ala-Gly copolypeptides, these materials have lamellar structures with two kinds of Ala residues in β-sheet, A and B, plus one distorted β-turn, t, formed by repetitive folding using β-turns every eighth amino acid in an antipolar arrangement. However, because of the presence of Ser residues at every sixth residue in (AGSGAG)n, the T1 values and mobilities of B decreased significantly. We conclude that the Ser hydroxyls hydrogen bond to adjacent lamellar layers and fix them together in a similar way to Velcro®.

Intramolecular and Intermolecular Packing in Polymer Crystallization

Recently, the chain-folding structure of 13C-labeled poly(l-lactic acid) (PLLA) with different molecular weights (M) of 46K (small, s), 90K (middle, m), and 320K g/mol (large, l) in the solution-gr...

Comparing Morphological Evolution during Tensile Deformation of Two Precise Polyethylenes via 2D Fitting of in Situ X-ray Scattering

Some types of precise polyethylenes, or linear polyethylenes containing precisely periodic functional groups, exhibit significant strain hardening under tensile deformation. Here we perform in situ X-ray scattering during tensile deformation of two precise polyethylenes: one with pendant carboxylic acid groups every 21st carbon (p21AA) and another with pendant imidazolium bromide groups every 15th carbon (p15ImBr). p21AA exhibits significant strain hardening and its layered structure orients with the layer normal along the tensile axis, while p15ImBr does not exhibit strain hardening and its layer normal orients perpendicular to the tensile axis. Quantitative evaluation of the 2D fiber patterns shows that p21AA undergoes a morphological transition, from a semicrystalline structure to a nanofibrillar structure, while the morphology of p15ImBr reorients and the chain folding structure is preserved. This suggests that fibrillization plays an important role in the strain hardening mechanism.

Chain Trajectory, Chain Packing, and Molecular Dynamics of Semicrystalline Polymers as Studied by Solid-State NMR.

Chain-level structure of semicrystalline polymers in melt- and solution-grown crystals has been debated over the past half century. Recently, 13C–13C double quantum (DQ) Nuclear Magnetic Resonance (NMR) spectroscopy has been successfully applied to investigate chain-folding (CF) structure and packing structure of 13C enriched polymers after solution and melt crystallization. We review recent NMR studies for (i) packing structure, (ii) chain trajectory, (iii) conformation of the folded chains, (iv) nucleation mechanisms, (v) deformation mechanism, and (vi) molecular dynamics of semicrystalline polymers.

Chain Trajectory of Semicrystalline Polymers As Revealed by Solid-State NMR Spectroscopy.

Over the last half century, a chain-folding structure of semicrystalline polymers has been debated in polymer science. Recently, 13C-13C double quantum (DQ) NMR spectroscopy combined with 13C selective isotope labeling has been developed to investigate re-entrance sites of the folded chains, mean values of adjacent re-entry number ⟨n⟩ and fraction ⟨F⟩ of semicrystalline polymers. This viewpoint highlights the versatile approaches of using solid-state (ss) NMR and isotope labeling for revealing (i) chain trajectory in melt- and solution-grown crystals, (ii) conformation of the folded chains in single crystals, (iii) self-folding in the early stage of crystallization, and (iv) unfolding of the folded chains under stretching.

Analysis of regulatory mechanism after ErbB4 gene mutation based on local modeling methodology.

ErbB4 is an oncogene belonging to the epidermal growth factor receptor family and contributes to the occurrence and development of multiple cancers, such as gastric, breast, and colorectal cancers. Therefore, studies of the regulation of ErbB4 in cancerigenic pathway will advance molecular targeted therapy. Advanced bioinformatic analysis softwares, such as ExPASy, Predictprotei, QUARK, and I-TASSER, were used to analyze the regulatory mechanism after ErbB4 gene mutation in terms of amino acid sequence, primary, secondary, and tertiary structure of the protein and upstream-downstream receptor/ligands. Mutation of the 19th and 113th amino acids at the carboxyl terminus of ErbB4 protein did not affect its biological nature, but its secondary structure changed and protein binding sites were near 2 mutational sites; moreover, after mutation introduction, additional binding sites were observed. Tertiary structure modeling indicated that local structure of ErbB4 was changed from an α helical conformation into a β chain folding structure; the α helical conformation is the functional site of protein, while active sites are typically near junctions between helical regions, thus the helical structures are easily destroyed and change into folding structures or other structures after stretching. Mutable sites of ErbB4 is exact binding sites where dimer formed with other epidermal growth factor family proteins; mutation enabled the ErbB4 receptor to bind to neuregulin 1 ligand without dimer formation, disrupting the signal transduction pathway and affecting ErbB4 function.

Molecular Structural Basis for Stereocomplex Formation of Polylactide Enantiomers in Dilute Solution.

Poly(l-lactide) (PLLA) and poly(d-lactide) (PDLA) alternatively pack with each other and form stereocomplex crystals (SCs). The crystal habits of SCs formed in the dilute solution highly depend on the molecular weight (⟨Mw⟩). In this study, we investigated chain-folding (CF) structure for 13C labeled PLLA (l-PLLA) chains in SCs with PDLAs that have either high or low ⟨Mw⟩s by employing an advanced Double Quantum (DQ) NMR. It was found that the ensemble average of the successive adjacent re-entry number ⟨n⟩ for the l-PLLA chains drastically change depending on ⟨Mw⟩s of the counter PDLA chains in the SCs. It was concluded that the CF structures of l-PLLA depending on ⟨Mw⟩s of PDLA determine the crystal habits of SCs.

Three-Dimensional Conformation of Folded Polymers in Single Crystals.

The chain-folding mechanism and structure of semicrystalline polymers have long been controversial. Solid-state NMR was applied to determine the chain trajectory of (13)C CH3-labeled isotactic poly(1-butene) (iPB1) in form III chiral single crystals blended with nonlabeled iPB1 crystallized in dilute solutions under low supercooling. An advanced (13)C-(13)C double-quantum NMR technique probing the spatial proximity pattern of labeled (13)C nuclei revealed that the chains adopt a three-dimensional (3D) conformation in single crystals. The determined results indicate a two-step crystallization process of (i) cluster formation via self-folding in the precrystallization stage and (ii) deposition of the nanoclusters as a building block at the growth front in single crystals.

Chain Trajectory and Crystallization Mechanism of a Semicrystalline Polymer in Melt- and Solution-Grown Crystals As Studied Using 13C–13C Double-Quantum NMR

The re-entrance sites, successive chain-folding number ⟨n⟩, and chain-folding fraction ⟨F⟩ of the chain-folding (CF) structure of 13C CH3-labeled isotactic poly(1-butene) (iPB1) with an weight-averaged molecular weight (⟨Mw⟩ = 37 K g/mol) in solution- and melt-grown crystals as a function of crystallization temperature (Tc) were determined using solid-state (SS) NMR. The solution- and melt-grown crystals possessed adjacent re-entry structures between the right- and left-handed stems along the (100) and (010) planes, which were invariant as a function of Tc. The adjacent re-entry structures in the former exhibited long-range order (⟨n⟩ ≥ 8) compared with that in the latter (⟨n⟩ ≥ 1.7–2). These results indicated that the concentration and entanglement of polymers play significant roles in the CF process and structural formation during the initial stage of crystallization, whereas kinetics does not. Transmission electron microscopy (TEM) revealed well-defined hexagonal and circular crystals grown from the solution state at Tc = 60 and ∼0 °C, respectively. The morphological and molecular-level structural data demonstrated that kinetics influences the structural formations of polymers differently at different length scales during crystallization. Moreover, SS-NMR, small-angle X-ray scattering (SAXS), and atomic force microscopy (AFM) indicated that the crystallinity (χc) and lamellar thickness (⟨lc⟩) of the melt-grown crystals are highly dependent on Tc, whereas in the solution-grown crystals, these parameters are independent of Tc. The experimental results and molecular dynamics, as reported in the literature, indicated that both χc and ⟨lc⟩ are primarily determined by the molecular dynamics of the stems after deposition of the chains on the growth front (late process).

Elucidation of the Chain-Folding Structure of a Semicrystalline Polymer in Single Crystals by Solid-State NMR.

Despite tremendous efforts over the last half-century to elucidate the chain-folding (CF) structure of semicrystalline polymers, the re-entrance sites of folded chains, the successive CF number n, and the adjacent re-entry fraction F have not been well characterized due to experimental limitations. In this report, 13C-13C double-quantum (DQ) NMR was used to determine for the first time the detailed CF structure of 13C CH3-labeled isotactic poly(1-butene) (iPB1) in solution-grown crystals blended with nonlabeled iPB1 across a wide range of crystallization temperatures (Tcs). Comparison of the results of DQ experiments and spin dynamics simulations demonstrated that the majority of individual chains possess completely adjacent re-entry structures at both Tc = 60 and ∼0 °C, as well as indicated that a low polymer concentration, not kinetics, leads to cluster formations of single molecules in dilute solution. The changes in crystal habits from hexagonal shapes at Tc = 60 °C to rounded shapes at ∼0 °C (kinetic roughness) are reasonably explained in terms of kinetically driven depositions of single molecule clusters on the growth front.

Ideal Polyethylene Nanocrystals

The water-soluble catalyst precursor [[(2,4,6-(3,5-(CF3)2C6H3)3-C6H2)-N═C(H)-(3-(9-anthryl)-2-O-C6H3)-κ(2)-N,O]Ni(CH3)(TPPTS)] (TPPTS = tri(sodiumphenylsulfonate)phosphine) polymerizes ethylene to aqueous dispersions of highly ordered nanoscale crystals (crystallinity χ(DSC) ≥ 90%) of strictly linear polyethylene (<0.7 methyl-branches/1000 carbon atoms, Mn = 4.2 × 10(5) g mol(-1)). SAXS in combination with cryo-TEM confirms this unusually high degree of order (χ(SAXS) = 82%) and shows the nanoparticles to possess a very thin amorphous layer on the crystalline lamella, just sufficient to accommodate a loop, but likely no entanglements. This ideal chain-folded structure is corroborated by annealing studies on the aqueous-dispersed nanoparticles, which show that the chain can move through the crystal as evidenced by lamella thickening without disturbing the crystalline order as concluded from an unaltered low thickness of the amorphous layers. These ideal chain-folded polyethylene nanocrystals arise from the crystallization in the confined environment of a nanoparticle and a deposition of the growing polymer chain on the crystal growth front as the chain is formed by the catalyst.

Folded-chain structure of cellulose II suggested by molecular dynamics simulation

We investigated the possibility of a folded-chain crystal of the cellulose II polymorph by molecular dynamics (MD) simulation. The molecular direction of cellulose chains in cellulose II is anti-parallel, which allows the crystal to have folded-chain packing. It is impossible for cellulose I to form such a structure due to its parallel up assembly. The folded-chain crystal of the cellulose II polymorph was suggested based on the following results: (1) the glucose residue with boat and skew boat ring conformations enabled the cellulose chain to form a hairpin turn; (2) the lattice parameters of the folded-chain crystal and original crystal were almost the same (deviations in the a, b, and γ parameters of both crystals were within 3%); (3) the folded-chain molecular sheet was as stable in a water medium as the extended-chain molecular sheet, and structural parameters such as the hydrogen bonding system and side chain conformation of both molecular sheets were almost the same, indicating that the folded-chain molecular sheet is an initial structure during crystallization of the folded-chain crystal.

Physics of engineered protein hydrogels

AbstractArtificially engineered proteins and synthetic polypeptides have attracted widespread interest as building blocks for polymer hydrogels. The biophysical properties of the proteins, such as molecular recognition abilities, folded chain structures, and sequence‐dependent thermodynamic behavior, enable advances in functional, responsive, and tunable gels. This review discusses the design of polymer hydrogels that incorporate protein domains, highlighting new challenges in polymer physics that are presented by this emerging class of materials. Five types of engineered protein hydrogels are discussed: (a) physically associating protein polymer gels, (b) amorphous artificially engineered protein networks, (c) engineered proteins with crystalline domains, (d) stretchable protein tertiary structures in gels, and (e) protein gels with biological recognition properties. The physics of the protein component and the physical properties of the resulting hydrogels are summarized, illustrating how advances in understanding these systems are leading to exciting novel biofunctional hydrogels. © 2013 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2013

The effect of temperature on nascent morphology of polyethylene polymerized over solution-phase flat model catalysts

Abstract The structure and morphology of polyethylene (PE) produced during solution polymerization using bis(imino)pyridyl metal catalysts supported by flat SiO 2 /Si(100) wafers were investigated by atomic force microscopy (AFM) and electron diffraction. Depending on the polymerization temperature, ranging from RT to 85 °C, different morphologies of the nascent PE have been observed. “Sea weed” like supermolecular structures are the predominant nascent morphologies of the PE polymerized at low temperatures. This should be associated with the high PE yield and high nucleation rate at low temperature; the catalyst is highly active and the PE macromolecules have low solubility in toluene and nucleate immediately after formation. With increasing polymerization temperature, e.g. at 60 or 70 °C, larger single crystals with roughly a lozenge shape but saw-tooth-like facets have been created. The multilayer overgrowth of the PE crystals demonstrates that the generated PE materials exceed what is required for single layer crystal growth. At 85 °C, decreasing crystal growth rate results in the formation of small PE single crystals. At the same time, the high solubility of the PE in toluene results in continuous diffusion of the macromolecules to the existing PE crystals and therefore single crystals in regular truncated lozenge shape have been formed. Electron diffraction indicates that in the whole temperature range, PE crystallizes in flat-on crystals in chain-folded structure with different chain folding stem length.

Coding coarse grained polymer model for LAMMPS and its application to polymer crystallization

We present a patch code for LAMMPS to implement a coarse grained (CG) model of poly(vinyl alcohol) (PVA). LAMMPS is a powerful molecular dynamics (MD) simulator developed at Sandia National Laboratories. Our patch code implements tabulated angular potential and Lennard-Jones-9-6 (LJ96) style interaction for PVA. Benefited from the excellent parallel efficiency of LAMMPS, our patch code is suitable for large-scale simulations. This CG-PVA code is used to study polymer crystallization, which is a long-standing unsolved problem in polymer physics. By using parallel computing, cooling and heating processes for long chains are simulated. The results show that chain-folded structures resembling the lamellae of polymer crystals are formed during the cooling process. The evolution of the static structure factor during the crystallization transition indicates that long-range density order appears before local crystalline packing. This is consistent with some experimental observations by small/wide angle X-ray scattering (SAXS/WAXS). During the heating process, it is found that the crystalline regions are still growing until they are fully melted, which can be confirmed by the evolution both of the static structure factor and average stem length formed by the chains. This two-stage behavior indicates that melting of polymer crystals is far from thermodynamic equilibrium. Our results concur with various experiments. It is the first time that such growth/reorganization behavior is clearly observed by MD simulations. Our code can be easily used to model other type of polymers by providing a file containing the tabulated angle potential data and a set of appropriate parameters. Program summary Program title: lammps-cgpva Catalogue identifier: AEDE_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEDE_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU's GPL No. of lines in distributed program, including test data, etc.: 940 798 No. of bytes in distributed program, including test data, etc.: 12 536 245 Distribution format: tar.gz Programming language: C++/MPI Computer: Tested on Intel-x86 and AMD64 architectures. Should run on any architecture providing a C++ compiler Operating system: Tested under Linux. Any other OS with C++ compiler and MPI library should suffice Has the code been vectorized or parallelized?: Yes RAM: Depends on system size and how many CPUs are used Classification: 7.7 External routines: LAMMPS ( http://lammps.sandia.gov/), FFTW ( http://www.fftw.org/) Nature of problem: Implementing special tabular angle potentials and Lennard-Jones-9-6 style interactions of a coarse grained polymer model for LAMMPS code. Solution method: Cubic spline interpolation of input tabulated angle potential data. Restrictions: The code is based on a former version of LAMMPS. Unusual features.: Any special angular potential can be used if it can be tabulated. Running time: Seconds to weeks, depending on system size, speed of CPU and how many CPUs are used. The test run provided with the package takes about 5 minutes on 4 AMD's opteron (2.6 GHz) CPUs.

The behavior of cellulose molecules in aqueous environments

Molecular motions of cellulose chains in aqueous environments were investigated by comparison with those in non-aqueous environments using molecular simulation techniques. The cellulose chains under non-aqueous conditions approached each other closely and then made tight aggregates that were formed by direct hydrogen bonding. Those in aqueous environments, such as in a bio-system, were separated from each other by water molecules and did not have direct hydrogen bonding between the cellulose chain molecules. Folded-chain structures were not found in either aqueous or non-aqueous environments that were somewhat crowded. In the aqueous system, the water molecules around the cellulose chains restricted their molecular motions and interrupted formation of direct, interchain hydrogen bonds. In the non-aqueous system, the cellulose chains approached each other closely and then made a tight cluster before the chain molecules could wind and bend. It was concluded that a very dilute solution of cellulose molecules in appropriate solvents is necessary to create folded-chain or random-coiled structures. We also confirmed that the driving force for making tight clusters of cellulose molecules in highly concentrated solutions is the energy of the hydrogen bonding created directly between the hydroxyl groups of the cellulose chains. These results strongly suggest that hydrogen bonding plays a very important role in the characteristics of cellulose molecules.

Structural changes in isothermal crystallization processes of synthetic polymers studied by time-resolved measurements of synchrotron-sourced X-ray scatterings and vibrational spectra

The structural changes occurring in the isothermal crystallization processes of polyethylene (PE), polyoxymethylene (POM), and vinylidene fluoridetrifluoroethylene (VDFTrFE) copolymer have been reviewed on the basis of our recent experimental data collected by the time-resolved measurements of synchrotron-sourced wide-angle (WAXS) and small-angle X-ray scatterings (SAXS) and infrared spectra. The temperature jump from the melt to a crystallization temperature could be measured at a cooling rate of 600–1,000°C/min, during which we collected the WAXS, SAXS, and infrared spectral data successfully at time intervals of ca. 10 sec. In the case of PE, the infrared spectral data clarified the generation of chain segments of partially disordered trans conformations immediately after the jump. These segments then became transformed into more-regular all-trans-zigzag forms, followed by the formation of an orthorhombic crystal lattice. At this stage, the generation of a stacked lamellar structure having an 800-A-long period was detected in the SAXS data. This structure was found to transfer successively to a more densely packed lamellar structure having a 400-A-long period as a result of the secondary crystallization of the amorphous region in-between the original lamellae. As for POM, the formation process of a stacked lamellar structure was essentially the same as that mentioned above for PE, as evidenced from the analysis of SAXS and WAXS data. The observation of morphology-sensitive infrared bands revealed the evolution of fully extended helical chains after the generation of lamellae having folded chain structures. We speculate that these extended chains exist as taut tie chains passing continuously through the neighboring lamellae. In the isothermal crystallization of VDFTrFE copolymer from the melt, a paraelectric high-temperature phase was detected at first and then it transferred into the ferroelectric low-temperature phase at a later stage. By analyzing the reflection profile of the WAXS data, the structural ordering in the high-temperature phase and the ferroelectric phase transition to the low-temperature phase of the multidomain structure were traced successfully.