Polymer Length Research Articles

Controllable Polymerization of N -Substituted β-Alanine N -Thiocarboxyanhydrides for Convenient Synthesis of Functional Poly(β-peptoid)s

Controllable Polymerization of <i>N</i> -Substituted β-Alanine <i>N</i> -Thiocarboxyanhydrides for Convenient Synthesis of Functional Poly(β-peptoid)s

Effect of Polymer Drag Reducer on Rheological Properties of Rocket Kerosene Solutions.

Adding drag reduction agent (DRA) to rocket kerosene is an effective way to reduce the pipeline resistance of rocket kerosene transportation systems. However, so far, there have been few research reports on the effect of DRA on the rheological properties of rocket kerosene solution, especially from a microscopic perspective. In this study, coarse-grained molecular dynamics simulations were conducted to investigate the rheological properties of rocket kerosene solutions with DRAs of different chain lengths and concentrations. The results showed that the viscosity of DRA—kerosene solution is generally higher than that of pure kerosene at a low shear rate, while with an increase in shear rate, the viscosity of DRA—kerosene solution decreases rapidly and finally tends to become similar to that of pure kerosene. The shear viscosity of DRA—kerosene solution increases with an increase in chain length and concentration of polymers. Through observing the morphologic change of DRA molecules and analyzing the radius of gyration and the mean-squared end-to-end distance of polymers, it was confirmed that the rheological properties of DRA—kerosene solutions are strongly related to the degree of entanglement of polymer chains. The simulation results provide microscopic insights into the rheological behavior of DRA—kerosene solutions and clarify the intrinsic relation between the morphologic change of polymer molecules and the rheological properties of DRA—kerosene solutions.

Expanding the Scope of Metastable Species in Hydrogen Bonding-Directed Supramolecular Polymerization.

We reveal unique hydrogen (H‐) bonding patterns and exploit them to control the kinetics, pathways and length of supramolecular polymers (SPs). New bisamide‐containing monomers were designed to elucidate the role of competing intra‐ vs. intermolecular H‐bonding interactions on the kinetics of supramolecular polymerization (SP). Remarkably, two polymerization‐inactive metastable states were discovered. Contrary to previous examples, the commonly assumed intramolecularly H‐bonded monomer does not evolve into intermolecularly H‐bonded SPs via ring opening, but rather forms a metastable dimer. In this dimer, all H‐bonding sites are saturated, either intra‐ or intermolecularly, hampering elongation. The dimers exhibit an advantageous preorganization, which upon opening of the intramolecular portion of the H‐bonding motif facilitates SP in a consecutive process. The retardation of spontaneous self‐assembly as a result of two metastable states enables length control in SP by seed‐mediated growth.

Importance of Carbohydrate Quality: What Does It Mean and How to Measure It?

Dietary carbohydrates are our main source of energy. Traditionally, they are classified based on the polymer length between simple and complex carbohydrates, which does not necessarily reflect their impact on health. Simple sugars, such as fructose, glucose, and lactose, despite having a similar energy efficiency and caloric content, have very distinct metabolic effects, leading to increased risk for various chronic diseases when consumed in excess. In addition, beyond the absolute amount of carbohydrate consumed, recent data point out that the food form or processing level can modulate both the energy efficiency and the cardiometabolic risk associated with specific carbohydrates. To account for both of these aspects—the quality of carbohydrates as well as its food form—several metrics can be proposed to help identifying carbohydrate-rich food sources and distinguish between those that would favor the development of chronic diseases and those that may contribute to prevent these. This review summarizes the findings presented during the American Society of Nutrition Satellite symposium on carbohydrate quality, in which these different aspects were presented.

Comprehensive view of microscopic interactions between DNA-coated colloids

The self-assembly of DNA-coated colloids into highly-ordered structures offers great promise for advanced optical materials. However, control of disorder, defects, melting, and crystal growth is hindered by the lack of a microscopic understanding of DNA-mediated colloidal interactions. Here we use total internal reflection microscopy to measure in situ the interaction potential between DNA-coated colloids with nanometer resolution and the macroscopic melting behavior. The range and strength of the interaction are measured and linked to key material design parameters, including DNA sequence, polymer length, grafting density, and complementary fraction. We present a first-principles model that screens and combines existing theories into one coherent framework and quantitatively reproduces our experimental data without fitting parameters over a wide range of DNA ligand designs. Our theory identifies a subtle competition between DNA binding and steric repulsion and accurately predicts adhesion and melting at a molecular level. Combining experimental and theoretical results, our work provides a quantitative and predictive approach for guiding material design with DNA-nanotechnology and can be further extended to a diversity of colloidal and biological systems.

From blue fluorescence to red fluorescence: Solid-state oxidative coupling polymerization of fluorene and anthracene or naphthalene

Through the solid-state oxidative coupling polymerization, a series of fluorene-co-anthracene copolymer (PFA) and fluorene-co-naphthalene copolymers (PFN) were synthesized using FeCl3 as the oxidant. The structures of the copolymers were characterized by FT-IR and 1H NMR spectra, showing the random structures composed of fluorene units and 9,10-anthracene units or 1,4-linked naphthalene units. The increasing fluorene units in the backbones resulted in the increasing crystallization of copolymers by XRD patterns. All the copolymers exhibited good thermal stability. The optical properties could be adjusted by using different fluorene and anthracene or naphthalene ratios. Moreover, the polymer concentrations that affected the photoluminescence emission ranged from blue light to red light. The concentration-induced discoloration property also could be observed from the copolymers on the filter paper of TLC plates. This is attributed to the change in the effective conjugation length of a single polymer and the formation of polymer aggregates and excimers. These unique properties endow the PFA and PFN with potential applications in optoelectronics. Especially, these polymers exhibit enhanced emissions and on/off fluorescent switching which senses THF vapor efficiently.

The influences of substrates' physical properties on enzymatic PET hydrolysis: Implications for PET hydrolase engineering.

Plastic pollution in diverse terrestrial and marine environments is a widely recognised and growing problem. Bio-recycling and upcycling of plastic waste is a potential solution to plastic pollution, as these processes convert plastic waste into useful materials. Polyethylene terephthalate (PET) is the most abundant plastic waste, and this material can be degraded by a class of recently discovered bacterial esterase enzymes known as PET hydrolases (PETase). Investigations of the enzymatic hydrolysis of diverse PET molecules have clearly revealed that the biodegradability of various PET substrates depends on both their chemical structure and physical properties, including polymer length, crystallinity, glass transition temperature, surface area, and surface charge. This review summarises the known impacts of crystallinity and other physical properties on enzymatic PET hydrolysis.

Method Matters: Exploring Alkoxysulfonate-Functionalized Poly(3,4-ethylenedioxythiophene) and Its Unintentional Self-Aggregating Copolymer toward Injectable Bioelectronics.

Injectable bioelectronics could become an alternative or a complement to traditional drug treatments. To this end, a new self-doped p-type conducting PEDOT-S copolymer (A5) was synthesized. This copolymer formed highly water-dispersed nanoparticles and aggregated into a mixed ion–electron conducting hydrogel when injected into a tissue model. First, we synthetically repeated most of the published methods for PEDOT-S at the lab scale. Surprisingly, analysis using high-resolution matrix-assisted laser desorption ionization-mass spectroscopy showed that almost all the methods generated PEDOT-S derivatives with the same polymer lengths (i.e., oligomers, seven to eight monomers in average); thus, the polymer length cannot account for the differences in the conductivities reported earlier. The main difference, however, was that some methods generated an unintentional copolymer P(EDOT-S/EDOT-OH) that is more prone to aggregate and display higher conductivities in general than the PEDOT-S homopolymer. Based on this, we synthesized the PEDOT-S derivative A5, that displayed the highest film conductivity (33 S cm–1) among all PEDOT-S derivatives synthesized. Injecting A5 nanoparticles into the agarose gel cast with a physiological buffer generated a stable and highly conductive hydrogel (1–5 S cm–1), where no conductive structures were seen in agarose with the other PEDOT-S derivatives. Furthermore, the ion-treated A5 hydrogel remained stable and maintained initial conductivities for 7 months (the longest period tested) in pure water, and A5 mixed with Fe3O4 nanoparticles generated a magnetoconductive relay device in water. Thus, we have successfully synthesized a water-processable, syringe-injectable, and self-doped PEDOT-S polymer capable of forming a conductive hydrogel in tissue mimics, thereby paving a way for future applications within in vivo electronics.

Efficient compressed database of equilibrated configurations of ring-linear polymer blends for MD simulations

To effectively archive configuration data during molecular dynamics (MD) simulations of polymer systems, we present an efficient compression method with good numerical accuracy that preserves the topology of ring-linear polymer blends. To compress the fraction of floating-point data, we used the Jointed Hierarchical Precision Compression Number - Data Format (JHPCN-DF) method to apply zero padding for the tailing fraction bits, which did not affect the numerical accuracy, then compressed the data with Huffman coding. We also provided a dataset of well-equilibrated configurations of MD simulations for ring-linear polymer blends with various lengths of linear and ring polymers, including ring complexes composed of multiple rings such as polycatenane. We executed 109 MD steps to obtain 150 equilibrated configurations. The combination of JHPCN-DF and SZ compression achieved the best compression ratio for all cases. Therefore, the proposed method enables efficient archiving of MD trajectories. Moreover, the publicly available dataset of ring-linear polymer blends can be employed for studies of mathematical methods, including topology analysis and data compression, as well as MD simulations.

Active dynamics of chromosome polymers

Mechanical manipulation of chromosomes, driven via the forces applied by microscopic motor proteins, is an active process essential for biological function. The enormous length of the chromatin polymer makes coarse-graining an important aspect in modeling chromosomes. Effective-equilibrium descriptions of coarse-grained chromosomes have been useful in understanding structural features, however, these models are limited by their equilibrium-like dynamics and a lack of connection to microscopic activity.

Assessing the Polymer Coil-Globule State from the Very First Spectral Modes.

The determination of the coil-globule transition of a polymer is generally based on the reconstruction of scaling laws, implying the need for samples from a rather wide range of different polymer lengths N. The spectral point of view developed in this work allows for a very parsimonious description of all the aspects of the finite-size coil-globule transition on the basis of the first two Rouse (cosine) modes only, shedding new light on polymer theory and reintroducing well-established spectral methods that have been surprisingly neglected in this field so far. Capturing the relevant configuration path features, the proposed approach enables one to determine the state of a polymer without the need of any information about the polymer length or interaction strength. Importantly, we propose an experimental implementation of our analysis that can be easily performed with modern fluorescent imaging techniques and would allow differentiation of coil or globule conformations by simply recording the positions of at least three discernible loci on the polymer.

External-induced self-assembly of semi-flexible polymers on spherical shell

Self-assembly behavior of semiflexible polymers on rigid spherical shell is investigated using the molecular dynamics (MD) simulation method. We find that the conformation of semiflexible polymers depends on the length of polymers and bending energy of polymer chains. For moderate adhesive strength and bending energy, the polymers aggregate into multiple clusters, each of which contains several parallel chains. Simultaneously, the self-assembly conformations, volley-ball, helical and tennis-ball state, form on spherical shell depend on the number of clusters. We quantify the self-assembly conformation and analysis its physical mechanics of formation. This work may provide a theoretical foundation for the future theories of conformation prediction and material fabrication.

Atomistic investigations of polymer-doxorubicin-CNT compatibility for targeted cancer treatment: A molecular dynamics study

Doxorubicin is cytotoxic anthracycline antibiotic drug used in cancer treatment. The drug’s efficacy in various kinds of cancer made its usage dominant for treating cancers. In this study, we determined the solubility of the doxorubicin in three different polymers, i.e., poly (N-isopropyl acrylamide), polyethylene glycol, and polyvinyl pyrrolidone, to increase the doxorubicin’s drug efficacy on the targeted tumor site. We investigated the doxorubicin-polymer interactions with carbon-nanotube in the aqueous environment for the targeted delivery application using classical molecular dynamics simulations. An in-depth atomistic insight into polymer interaction with the drug/carbon-nanotube/water is obtained within the study. We have critically analyzed various properties such as interaction energy, hydrogen bonds between polymer-drug and polymer-water, the diffusion coefficient of the drug, end-to-end distance, radius of gyration of the polymer chains, and finally, drug density contours for different drug to polymer ratios. Our results explain the selection of effective monomer chain length of polymer and the suitability of the polymer carrier with doxorubicin.

Multivalent polymers can control phase boundary, dynamics, and organization of liquid-liquid phase separation.

Multivalent polymers are a key structural component of many biocondensates. When interacting with their cognate binding proteins, multivalent polymers such as RNA and modular proteins have been shown to influence the liquid-liquid phase separation (LLPS) boundary to both control condensate formation and to influence condensate dynamics after phase separation. Much is still unknown about the function and formation of these condensed droplets, but changes in their dynamics or phase separation are associated with neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and Alzheimer’s Disease. Therefore, investigation into how the structure of multivalent polymers relates to changes in biocondensate formation and maturation is essential to understanding and treating these diseases. Here, we use a coarse-grain, Brownian Dynamics simulation with reactive binding that mimics specific interactions in order to investigate the difference between non-specific and specific multivalent binding polymers. We show that non-specific binding interactions can lead to much larger changes in droplet formation at lower protein-polymer interaction energies than their specific, valence-limited counterparts. We also demonstrate the effects of solvent conditions and polymer length on phase separation, and we present how modulating binding energy to the polymer can change the organization of a droplet in a three component system of polymer, binding protein, and solvent. Finally, we compare the effects of surface tension and polymer binding on the condensed phase dynamics, and show that both lower protein solubilities and higher attraction/affinity of the protein to the polymer result in slower droplet dynamics. This research will help to better understand experimental systems and provides additional insight into how multivalent polymers can control LLPS.

The bacterial tyrosine kinase system CpsBCD governs the length of capsule polymers

Many pathogenic bacteria are encased in a layer of capsular polysaccharide (CPS). This layer is important for virulence by masking surface antigens, preventing opsonophagocytosis, and avoiding mucus entrapment. The bacterial tyrosine kinase (BY-kinase) regulates capsule synthesis and helps bacterial pathogens to survive different host niches. BY-kinases autophosphorylate at the C-terminal tyrosine residues upon external stimuli, but the role of phosphorylation is still unclear. Here, we report that the BY-kinase CpsCD is required for growth in Streptococcus pneumoniae Cells lacking a functional cpsC or cpsD accumulated low molecular weight CPS and lysed because of the lethal sequestration of the lipid carrier undecaprenyl phosphate, resulting in inhibition of peptidoglycan (PG) synthesis. CpsC interacts with CpsD and the polymerase CpsH. CpsD phosphorylation reduces the length of CPS polymers presumably by controlling the activity of CpsC. Finally, pulse-chase experiments reveal the spatiotemporal coordination between CPS and PG synthesis. This coordination is dependent on CpsC and CpsD. Together, our study provides evidence that BY-kinases regulate capsule polymer length by fine-tuning CpsC activity through autophosphorylation.

MP-NeRF: A massively parallel method for accelerating protein structure reconstruction from internal coordinates.

The conversion of proteins between internal and cartesian coordinates is a limiting step in many pipelines, such as molecular dynamics simulations and machine learning models. This conversion is typically carried out by sequential or parallel applications of the Natural extension of Reference Frame (NeRF) algorithm. This work proposes a massively parallel NeRF implementation which, depending on the polymer length, achieves speedups between 400 and 1200× over the previous state-of-the-art. It accomplishes this by dividing the conversion into three main phases: parallel composition of the monomer backbone, assembly of backbone subunits, and parallel elongation of sidechains; and by batching these computations into a minimal number of efficient matrix operations. Special emphasis is placed on reusability and ease of use. We open source the code (available at https://github.com/EleutherAI/mp_nerf) and provide a corresponding python package.

Structural aspects of a self-emulsifying multifunctional amphiphilic excipient: Part II. The case of Cremophor EL

Lipids and lipid-based excipients, such as Cremophor EL used in this study, play an important role in improving the solubility of poorly soluble drugs and drug candidates. The use of such excipients in self-emulsifying formulations has been widely reported in the literature. In the current study, we report the micellar behavior of Cremophor EL at several concentrations (above the critical micelle concentration) and temperatures using small-angle neutron scattering. For all conditions, Cremophor EL formed core–shell spherical micelles with an overall radius of ∼ 50 Å, a hydrophobic core radius of ∼ 25 Å, and a shell thickness of ∼ 23 Å with a polydispersity of ∼ 25%. The thickness of the shell (equivalent to the polymer length in the brush regime), and consequently of the overall micelle, was found to increase with increasing temperature. This study will aid our understanding of how drugs could interact with lipid excipients and how such drug-excipient mixtures behave during manufacture, storage, and after administration.

Mask, the Drosophila ankyrin repeat and KH domain-containing protein, affects microtubule stability.

ABSTRACTProper regulation of microtubule (MT) stability and dynamics is vital for essential cellular processes, including axonal transportation and synaptic growth and remodeling in neurons. In the present study, we demonstrate that the Drosophila ankyrin repeat and KH domain-containing protein Mask negatively affects MT stability in both larval muscles and motor neurons. In larval muscles, loss-of-function of mask increases MT polymer length, and in motor neurons, loss of mask function results in overexpansion of the presynaptic terminal at the larval neuromuscular junctions (NMJs). mask genetically interacts with stathmin (stai), a neuronal modulator of MT stability, in the regulation of axon transportation and synaptic terminal stability. Our structure–function analysis of Mask revealed that its ankyrin repeats domain-containing N-terminal portion is sufficient to mediate Mask's impact on MT stability. Furthermore, we discovered that Mask negatively regulates the abundance of the MT-associated protein Jupiter in motor neuron axons, and that neuronal knocking down of Jupiter partially suppresses mask loss-of-function phenotypes at the larval NMJs. Taken together, our studies demonstrate that Mask is a novel regulator for MT stability, and such a role of Mask requires normal function of Jupiter.

Mechanical grinding alters physicochemical, structural, and functional properties of tobacco (Nicotiana tabacum L.) leaf powders

Utilizing tobacco industrial waste can increase added value without increasing the environmental burden. The physicochemical, structural, and functional properties of tobacco leaf powders produced by coarse and superfine grinding treatments with different particle size were investigated. The particle size was significantly reduced by superfine grinding to micron scale (10.3 μm), and the specific surface area sharply increased. With decreasing particle size, the bulk density, tap density, angles of repose and slide increased, but water and oil holding capacities decreased, indicating the worse flowability and hydration property. The increasing lightness and yellowness but decreasing redness were observed after superfine grinding. Differential scanning calorimetry curves showed that superfine grinding insignificantly affected the conformation stability and denaturation degree of proteins. Fourier transform infrared spectroscopy proved unchanged main structure and decreased chain length of polysaccharide polymer. Morphology revealed that the shape of superfine ground sample was changed from an irregular polygon to spherical-like, and surface roughness was reduced. All cell walls were disrupted after superfine grinding, but the dissolution yields of nicotine and total phenolic, and antioxidant activities were not enhanced. The median particle size of 93.9 μm was the most effective for the ingredient dissolution and antioxidant capacity. This study was expected to supply new insights in guiding the development of discarded tobacco in practice.

Tuning the Properties of Surface-Anchored Polymer Networks by Varying the Concentration of a Thermally Activated Cross-Linker, Annealing Time, and Temperature in a One-Pot Reaction

We investigate the properties of surface-anchored polymer networks created via one-pot synthesis using thermally active 6-azidosulfonylhexyltriethoxysilane (6-ASHTES). 6-ASHTES is a bifunctional gelator that undergoes cross-linking and surface-anchoring reactions when annealed above 100 °C. We employ a poly(vinylpyrrolidone) (PVP) with different molecular weights (10–1300 kDa) as a model system to examine the effect of 6-ASHTES concentration, annealing time, and annealing temperature on gel formation. A thin film of PVP/6-ASHTES mixture is deposited on a clean silicon wafer and annealed to form network layers. Spectroscopic ellipsometry measures the film thickness of the cross-linked layers from which the gel fraction and swelling ratio are determined. The gel fraction of PVP in the network can be “dialed in” by varying the annealing time, temperature, and concentration of 6-ASHTES in the PVP/6-ASHTES mixture. We use a simple Monte Carlo simulation model to describe cross-linking as a function of cross-linker concentration, reaction rate, reaction time, and polymer length. The trends obtained from the model simulations are in qualitative agreement with the experimental data.