Chain Conformation Research Articles

Molecular dynamics simulation of stretching-induced ductility for polystyrene

Some glassy polymers have a mechanical behavior that stretching can induce the brittle-to-ductile transition (BDT). For polystyrene (PS) film, after pre-stretching above glass transition temperature (Tg), the property at room temperature transforms to ductile, showing higher elongation at break and higher yield strength. In this work, we have investigated this phenomenon of stretching induced ductility by molecular dynamics (MD) analysis referring to our experimental findings. PS specimens in united-atom model with different chain lengths were loaded by deformation at two-step temperature setting, which was 393 K at first and then 300 K, to simulate tensile behaviors with various per-stretching conditions. The result has shown that as deformations beginning at 393 K and proceeding at 300 K, root mean square radius of gyration (Rg) and the degree of orientation (P2,x) reach the maximum value higher than solely stretching at 393 K or 300 K. Therefore, the stretching-induced BDT is attributed to changing of both chain conformation and coil configuration in polymer chains in stepwise stretching, which can change their coil configuration at the pre-stretching, adjusting their chain network in a more stretchable position, leading the whole polymer amorphous from brittle to ductile. The simulation result is accordant with our experiment and previous BDT theory to glassy polymers.

Quantification of Distributions of Local Proton Concentrations in Heterogeneous Soft Matter and Non-Anfinsen Biomacromolecules.

A new method to quantitatively analyze heterogeneous distributions of local proton densities around paramagnetic centers in unstructured and weakly structured biomacromolecules and soft matter is introduced, and its feasibility is demonstrated on aqueous solutions of stochastically spin-labeled polysaccharides. This method is based on the pulse EPR experiment ih-RIDME (intermolecular hyperfine relaxation-induced dipolar modulation enhancement). Global analysis of a series of RIDME traces allows for a mathematically stable transformation of the time-domain data to the distribution of local proton concentrations. Two pulse sequences are proposed and tested, which combine the ih-RIDME block and the double-electron-electron resonance (DEER) experiment. Such experiments can be potentially used to correlate the local proton concentration with the macromolecular chain conformation. We anticipate an application of this approach in studies of intrinsically disordered proteins, biomolecular aggregates, and biomolecular condensates.

Preparation of hyperbranched hydrophobic nano-silica and its superior needling-effect in PDMS defoam agent

Hydrophobic nano silica powder is a kind of important synergist to silicone defoaming agents. The large pore volume and branched chain conformation of silica nanoparticles present superior effects on defoaming properties. However, silica nanoparticles synthesized by liquid phase easily aggregate and pore collapse because of their high surface activity and polarity, leading to poorer dispersity and limited practicability. In this paper, a novel hydrophobic silica with a hyperbranched structure was designed through in-situ modifying method with hexamethyldisilazane (HMDS) and polydimethylsiloxane (PDMS) in the liquid phase. The trimethylsilanol generated by HMDS hydrolysis reacts quickly with the highly active hydroxyl groups on the silica, causing the surface properties of the nanoparticles to transform from polar to non-polar properties. The steric hindrance of the trimethyl silicon and the reduction of the surface polarity effectively prevent silica pores from collapsing and maintain the macropore structures to realize the hyperbranched silica. At the same time, the −Si (CH3)2− from PDMS endowed the hyperbranched silica with excellent hydrophobicity. When applied in the defoaming agent, the hydrophobicity of silica contributes to dewetting the foams, and the hyperbranched spatial structures play an enhanced needling effect. Therefore, this hydrophobic hyperbranched silica exhibited a surprising defoaming effect, which significantly reduced the defoaming time from 464.4 s to less than 2 s, superior to commercial defoaming silica (155.3 s). The defoaming efficiency reached 100 % within 2 s of the end of the shaking, and the defoamer antifoaming ability was improved to reach 27.5 min, which was 77 % higher than that of commercial defoamer.

POSoligo software for in vitro gene synthesis

Oligonucleotide synthesis is vital for molecular experiments. Bioinformatics has been employed to create various algorithmic tools for the in vitro synthesis of nucleotides. The main approach to synthesizing long-chain DNA molecules involves linking short-chain oligonucleotides through ligase chain reaction (LCR) and polymerase chain reaction (PCR). Short-chain DNA molecules have low mutation rates, while LCR requires complementary interfaces at both ends of the two nucleic acid molecules or may alter the conformation of the nucleotide chain, leading to termination of amplification. Therefore, molecular melting temperature, length, and specificity must be considered during experimental design. POSoligo is a specialized offline tool for nucleotide fragment synthesis. It optimizes the oligonucleotide length and specificity based on input single-stranded DNA, producing multiple contiguous long strands (COS) and short patch strands (POS) with complementary ends. This process ensures free 5′- and 3′-ends during oligonucleotide synthesis, preventing secondary structure formation and ensuring specific binding between COS and POS without relying on stabilizing the complementary strands based on Tm values. POSoligo was used to synthesize the linear RBD sequence of SARS-CoV-2 using only one DNA strand, several POSs for LCR ligation, and two pairs of primers for PCR amplification in a time- and cost-effective manner.

Reusable and effective polyacrylic membranes for mecoprop and bentazon extractions

This study introduces reusable polyacrylic membranes, fabricated from commercially available monomers (1-vinyl-2-pyrrolidone and methylmethacrylate), as a promising approach for pesticide extraction. These membranes effectively remove the commonly used herbicides mecoprop (RE ≈ 99%) and bentazon (RE ≈ 95%) at low concentrations, which pose water contamination risks due to their water-soluble properties and leaf-level sorption. The membranes exhibit excellent manageability and resistance, allowing for safe handling without personal protective equipment. Additionally, the material is environmentally friendly and can be washed and reused for at least 4 cycles without a significant decrease in performance. Characterization techniques, including NMR, TGA, DSC, mechanical testing, N2 adsorption, and FTIR analysis, were used to investigate properties and assess the influence of the polymeric composition. The study focused on examining the lateral charged aminoethyl groups, which play a crucial role in sorbent-sorbate interactions. Sorption kinetics, isotherms, and permeation studies provided insights into the removal mechanism, efficiency, and permeability coefficients, revealing hydrophobic–hydrophobic interactions between the pesticides and the polymer. Molecular dynamics simulations revealed a scorpion-like conformation of the macromolecular chains surrounding the pesticides. These findings support the hydrophobic nature of the extraction mechanism and highlight the significant role of charged aminoethyl groups in facilitating this process.

Metal-Halogen Interactions Inducing Phase Separation for Self-Healing and Tough Ionogels with Tunable Thermoelectric Performance.

Ionic liquid-based thermoelectric gels become a compelling candidate for thermoelectric power generation and sensing due to their giant thermopower, good thermal stability, high flexibility, and low-cost production. However, the materials reported to date suffer from canonical trade-offs between self-healing ability, stretchability, strength, and ionic conductivity. Herein, a self-healing and tough ionogel (PEO/LiTFSI/EmimCl) with tunable thermoelectric properties by tailoring metal-halogen bonding interactions, is developed. Different affinities between polymer matrix and salts are exploited to induce phase separation, resulting in simultaneous enhancement of ionic conductivity and mechanical strength. Molecular dynamics (MD) simulations and spectroscopic analyses show that Cl- ions impair the lithium-ether oxygen coordination, leading to changes in chain conformation. The migration difference between cations and anions is thus widened and a transition from n-type to p-type thermoelectric ionogels is realized. Furthermore, the dynamic interactions of metal-ligand coordination and hydrogen bonding yield autonomously self-healing capability, large stretchability (2000%), and environment-friendly recyclability. Benefiting from these fascinating properties, the multifunctional PEO-based ionogels are applied in sensors, supercapacitors, and thermoelectric power generation modules. The strategy of tuning solvation dominance to address the trade-offs in thermoelectric ionogels and optimize their macroscopic properties offers new possibilities for the design of advanced ionogels.

Distribution of Density of States in Organic Field–Effect Transistors Based on Polymer Dielectrics

AbstractThe distribution of density of states (DOS) holds fundamental importance in determining charge transport within organic field–effect transistors (OFETs). Herein, the modulation of DOS distribution in OFET devices is demonstrated by altering the chain conformation of the polymer dielectrics. A rapid film‐formation technique, specifically the spin‐casting method, is used to fabricate the dielectric layer using poly(methyl methacrylate) (PMMA). This method allows for the retention of some memory of the chain conformations from the solution to the resulting dry film. This memory effect is employed to prepare thin PMMA films with different local chain conformations by adjusting the quality of the solvent. Good solvent forms solidified films with a reduced amount of gauche conformer in the PMMA chain, resulting in a narrow DOS distribution width. Consequently, the device exhibited enhanced charge mobility and a reduced subthreshold swing. The observed change in the width of the DOS distribution can be attributed to the alteration of the local energy state of the semiconductor, induced by the local chain conformation of PMMA dielectrics through electrostatics and steric interactions.

Synergistic effects of nucleating agent, chain extender and nanocrystalline cellulose on PLA and PHB blend films: Evaluation of morphological, mechanical and functional attributes

The current study focuses on reactive extrusion of poly (lactic acid) (PLA) and polyhydroxybutyrate (PHB) based blend films using epoxide styrene–acrylic (ESA) chain extender, pentaerythritol (PEOL) as a nucleating agent and cellulose nanocrystal (CNC). The blown films were subjected to various mechanical, thermal, barrier, and microstructural analyses to determine their suitability for packaging. Test results indicated that the incorporation of 0.5 wt% of chain extender significantly improved the elastic modulus and yield strength of PLA/PHB blend films. Further addition of 1 wt% of PEOL improved the crystallinity as well as mechanical strength in the films. FTIR analysis suggested chain conformations in different crystalline regions of PLA/PHB blend films whereas nucleation density and arrangement in crystal growth have been analysed by POM and SEM micro graphical studies. Additionally, the presence of CNCs within the PLA/PHB blend films showed an improved water vapour transmission rate (WVTR) of 90.53 g/m2.day revealing the creation of a tortuous path. Evaluation of optimum glossiness and haze of the films were done and the co-efficient of friction analysis depicted more anti-slip properties of the films.

Role of the Chain Structure and Conformation of Conjugated Polymers on Aggregation Behavior

Role of the Chain Structure and Conformation of Conjugated Polymers on Aggregation Behavior

Host-Guest Interaction Mediated Interfacial Co-Assembly of Cyclodextrin and Bottlebrush Surfactants for Precisely Tunable Photonic Supraballs.

Investigations of host-guest interactions at water-oil (w/o) interfaces are limited in single emulsion systems producing simple self-assembled objects with limited uses. Here, within hierarchically ordered water-in-oil-in-water (w/o/w) multiple emulsion droplets, interfacial self-assembly of (polynorbornene-graft-polystyrene)-block-(polynorbornene-graft-polyethylene glycol) (PNPS-b-PNPEG) bottlebrush block copolymers can be precisely controlled through host-guest interactions. α-Cyclodextrin (α-CD) in the aqueous phase can thread onto PEG side chains of the bottlebrush surfactants adsorbed at the w/o interface, leading to dehydration and collapsed chain conformation of the PEG block. Consequently, spherical curvature of the w/o internal droplets increases with the increased asymmetry of the bottlebrush molecules, producing photonic supraballs with precisely tailored structural parameters as well as photonic bandgaps. This work provides a simple but highly effective strategy for precise manipulation of complex emulsion systems applicable in a variety of applications, such as photonic pigments, cosmetic products, pesticides, artificial cells, etc.

Hemostatic and Ultrasound-Controlled Bactericidal Silk Fibroin Hydrogel via Integrating a Perfluorocarbon Nanoemulsion.

Excessive blood loss and infections are the prominent risks accounting for mortality and disability associated with acute wounds. Consequently, wound dressings should encompass adequate adhesive, hemostatic, and bactericidal attributes, yet their development remains challenging. This investigation presented the benefits of incorporating a perfluorocarbon nanoemulsion (PPP NE) into a silk-fibroin (SF)-based hydrogel. By stimulating the β-sheet conformation of the SF chains, PPP NEs drastically shortened the gelation time while augmenting the elasticity, mechanical stability, and viscosity of the hydrogel. Furthermore, the integration of PPP NEs improved hemostatic competence by boosting the affinity between cells and biomacromolecules. It also endowed the hydrogel with ultrasound-controlled bactericidal ability through the inducement of inner cavitation by perfluorocarbon and reactive oxygen species (ROS) generated by the sonosensitizer protoporphyrin. Ultimately, we employed a laparotomy bleeding model and a Staphylococcus aureus-infected trauma wound to demonstrate the first-aid efficacy. Thus, our research suggested an emulsion-incorporating strategy for managing emergency wounds.

Modulation of Phase Separation Morphology by Configuration Engineering in Bulk Heterojunction Organic Solar Cells

For bulk‐heterojunction organic solar cells (OSCs), molecular structure design to control molecular stacking is crucial to obtain ideally phase‐separated morphology and high device performance. Herein, the investigation focuses on two polythiophene‐quinoxaline (PTQ) derivatives (PTQ8 and PTQ10) blended with Y6, utilizing coarse‐grained molecular dynamics simulations based on the Lennard–Jones static potential (LJSP) method. The study reveals that the diminished photovoltaic efficiencies of PTQ8:Y6 blends, compared to PTQ10:Y6 blends, are not solely attributed to reduced driving forces. The introduction of fluorine‐substituted sites in the thiophene group of PTQ polymer is identified as a significant factor. This alteration causes PTQ polymers in PTQ8:Y6 blends to coil, compromising the crystalline structure. PTQ8's bifluorine group induces a repulsive effect on the quinoxaline group, leading to a coiled‐chain structure that hinders chain stacking. Conversely, PTQ10 exhibits a straighter chain conformation. Additionally, PTQ8's high solubility in chloroform prevents effective aggregation, further impeding suitable morphology formation. Coarse‐grained simulations employing LJSP prove effective in precisely exploring the morphology of OSCs, offering crucial insights for materials in this field.

Evaluation of free radical‐induced structural changes and their effect on antioxidant and anti‐inflammatory activities of UV/H2O2‐degraded dextrans

AbstractAlthough ultraviolet (UV)/H2O2 treatment could effectively improve the bioactivities of polysaccharides, the relationship between free radical‐induced structural changes and the bioactivities of products remains unknown. Therefore, this work investigated the changes in the chemical characteristics and chain conformations of degraded dextrans by the UV/H2O2 system as well as their antioxidant and anti‐inflammatory activities. The apparent degradation efficiencies of dextrans under different UV/H2O2 parameters were first investigated. UV/H2O2 treatment effectively destroyed the pyranose rings and glycosidic bonds of dextrans and significantly improved their uronic acid and carboxy contents. Furthermore, conformational studies revealed that besides the rapid decrease in the molecular weight, the compact spherical conformation of dextrans was gradually depolymerized into the flexible random coil conformation. Moreover, the significant antioxidant and anti‐inflammatory activities of the degraded dextrans were mainly attributed to their more extended random coil chains, increased quantity of reducing groups, and lower molecular sizes. This study contributes to investigating the structure–activity relationship of polysaccharides prepared by free radicals‐mediated degradation.

Spring Lock: Constructing Cluster Emitters with Colorful TADF from Non‐Conjugated Polymaleimide Helical Chains

AbstractNon‐conjugated luminescent polymers have received much attention due to their excellent flexibility, processability, and biocompatibility. However, the single emission color and low solid‐state luminescence efficiency restrict their further development. Herein, by introducing carboxyl‐terminated alkyl chains on the rigid and helical polymaleimide backbone, a series of non‐conjugated luminescent polymers are designed and synthesized. Due to the “spring lock” formed by the synergism of scalable helical main chains and flexible alkyl side chains, these polymers exhibit effective cluster luminescence with thermally activated delayed fluorescence (TADF) property, thereby significantly improving the solid‐state luminescence efficiency with the quantum yield up to 59.6%. The TADF emission wavelengths of the polymer powders can be tuned from 498 to 639 nm through changing reaction solvents, because the conformation of helical chains forming clusters is sensitive to solvent polarity. Interestingly, metal ions can induce the polymers to construct self‐repairing cluster luminescence gels, which show excellent potential applications in ammonia detection and information encryption. This work not only provides an effective design strategy for the colorful cluster luminescence with high‐efficiency TADF, but also further reveals the cluster luminescence mechanism and enlightens the promising applications of cluster luminescent gels.

Characterizing the shear response of polymer-grafted nanoparticles.

Grafting polymer chains to the surface of nanoparticles overcomes the challenge of nanoparticle dispersion within nanocomposites and establishes high-volume fractions that are found to enable enhanced material mechanical properties. This study utilizes coarse-grained molecular dynamics simulations to quantify how the shear modulus of polymer-grafted nanoparticle (PGN) systems in their glassy state depends on parameters such as strain rate, nanoparticle size, grafting density, and chain length. The results are interpreted through further analysis of the dynamics of chain conformations and volume fraction arguments. The volume fraction of nanoparticles is found to be the most influential variable in deciding the shear modulus of PGN systems. A simple rule of mixture is utilized to express the monotonic dependence of shear modulus on the volume fraction of nanoparticles. Due to the reinforcing effect of nanoparticles, shortening the grafted chains results in a higher shear modulus in PGNs, which is not seen in linear systems. These results offer timely insight into calibrating molecular design parameters for achieving the desired mechanical properties in PGNs.

Early screening of colorectal cancer using feature engineering with artificial intelligence-enhanced analysis of nanoscale chromatin modifications

Colonoscopy is accurate but inefficient for colorectal cancer (CRC) prevention due to the low (~ 7 to 8%) prevalence of target lesions, advanced adenomas. We leveraged rectal mucosa to identify patients who harbor CRC field carcinogenesis by evaluating chromatin 3D architecture. Supranucleosomal disordered chromatin chains (~ 5 to 20 nm, ~1 kbp) fold into chromatin packing domains (~ 100 to 200 nm, ~ 100 to 1000 kbp). In turn, the fractal-like conformation of DNA within chromatin domains and the folding of the genome into packing domains has been shown to influence multiple facets of gene transcription, including the transcriptional plasticity of cancer cells. We deployed an optical spectroscopic nanosensing technique, chromatin-sensitive partial wave spectroscopic microscopy (csPWS), to evaluate the packing density scaling D of the chromatin chain conformation within packing domains from rectal mucosa in 256 patients with varying degrees of progression to colorectal cancer. We found average packing scaling D of chromatin domains was elevated in tumor cells, histologically normal-appearing cells 4 cm proximal to the tumor, and histologically normal-appearing rectal mucosa compared to cells from control patients (p < 0.001). Nuclear D had a robust correlation with the model of 5-year risk of CRC with r2 = 0.94. Furthermore, rectal D was evaluated as a screening biomarker for patients with advanced adenomas presenting an AUC of 0.85 and 85% sensitivity and specificity. artificial intelligence-enhanced csPWS improved diagnostic performance with AUC = 0.90. Considering the low sensitivity of existing CRC tests, including liquid biopsies, to early-stage cancers our work highlights the potential of chromatin biomarkers of field carcinogenesis in detecting early, significant precancerous colon lesions.

Influence of Lipid Conformations on the Interaction Energy between a Membrane and a Peripheral Protein

Peripheral membrane proteins are temporarily coupled to the surface of a membrane, penetrating into the lipid layer. In this work, it has been shown that the fraction of trans configurations of dihedral angles in hydrophobic chains of lipids decreases in the region of contact of peripheral membrane proteins with the membrane. This effect differs for different lipid chains and for dihedral angles at different distances from the beginning of a chain. A gosh configuration has a higher energy than a trans configuration. Consequently, the decrease in the fraction of trans configurations leads to an increase in the energy of the chain. The energy of chain conformations for the peripheral membrane protein considered in this work increases by ≈2 kJ/mol. A chain in chain conformations is involved in molecular mechanisms determining the elastic modulus of membranes. The energy stored in a conformation chain can be spent to the desorption of protein from the surface of the membrane and can be considered as a reason why the interaction of peripheral membrane proteins with the membrane is temporal.

Conformational Diversity of Lipids

The conformational diversity of hydrophobic lipid chains has been studied. The number of possible conformations of a lipid chain, as well as the number of these conformations that can be realized in a real system, has been determined. A set theory approach to the analysis of conformations of lipid molecules has been proposed, and a relation of the sets of conformations realized in a lipid structure to the energy of the system has been introduced. Using the set theory, it has been considered which conformations of hydrophobic lipid chains can be realized in the real system. The notion of the key conformation has been formulated to estimate the correlation between the structural characteristics of lipids and the energy characteristics of membranes.

Prediction of the second critical micelle concentration of aqueous tween and span solutions via CPA EoS: Application of the quantitative theory in growth of wormlike micelles

A new combination of previously established molecular-thermodynamic methods was offered in conjunction with the Cubic Plus Association (CPA) equation of state (EoS) for the assessment of the second critical micelle concentration (SCMC), and curvature parameters in aqueous solutions of non-ionic surfactants encompassing Tween 80, Tween 60, Span 80, and Span 60. This combination will yield a quantifiable examination that adheres to creating the micelles resembling worms, enabling the optimization of critical curvature parameters, as well as the prediction of the SCMC. This previously well-known model is reliant upon theoretical components, including chain conformation, headgroup-steric effects, and interfacial tension pertaining to the energy of micelle-free systems. So, the optimized curvature parameters obtained because of these forces can be used as the input of CPA EoS to independently count the association interactions and predict the SCMC for the first time. For the aforementioned surfactants, the first critical micelle concentration (FCMC) data was previously used to modify five pure parameters of the CPA EoS. Consequently, applying the adjusted parameters, the SCMC of noted aqueous solutions has been predicted reasonably using CPA EoS.

Cold crystallization of polytrimethylene terephthalate and copolymers

The melt of crystalline polymers normally crystalize on cooling and the polymer melts with low critical cooling rate would easily solidify as glass during cooling to their glass transition temperature (Tg). The glassy process exhibits variety within each kind of polymer melts in the slope of the viscosity-temperature visibility, and the rate of the excess conformational entropy in the polymer melt over the crystalline phase changes in the Tg approaching. Polytrimethylene terephthalate (PTT) and a series of polytrimethylene terephthalate copolyesters (PTTG) with different molar ratios of 1,3-propylene glycol (1,3-PDO) to 1,4-cyclohexanedimethanol (1,4-CHDM) were synthesized to modify the chain flexibility and the critical cooling rate. The glassy samples were obtained via quenching the melts of PTT and copolymers below the Tg to characterize the cold crystallization behaviors. The evolutions of the crystalline structure of the amorphous samples were in situ investigated via DSC and simultaneous WAXS/SAXS approaches during heating. The polymer chain dynamics and the critical cooling rates of the PTT and copolymers were estimated by rheological testing and DSC characterization. The results indicate that the chain conformation adjustment of PTT and copolymers is relate to the comonomers in the copolymers, and the cold crystallization behaviors can be divided into three temperature ranges during heating. The first involves rapid transition from a pre-ordered phase to a crystalline phase, the second is the adjustment of defects in an imperfect crystalline phase, and the third may refer crystal reorganization before melting. The crystallization ability of the samples could be due to the ability of chain conformation adjustment with comonomer content till the crystallization is no longer obvious during heating. The cold crystallization behaviors of the samples were discussed based on the polymer chain dynamics and it is convinced that would be helpful to understand the crystallization and processing of polymers.