Chain Conformation Research Articles

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.

Anion-modulated Ion Conductor with Chain Conformational Transformation for stabilizing Interfacial Phase of High-Voltage Lithium Metal Batteries.

In solid-state lithium metal batteries (SSLMBs), the inhomogeneous electrolyte-electrode interphase layer aggravates the interfacial stability, leading to discontinuous interfacial ion/charge transport and continuous degradation of the electrolyte. Herein, we constructed an anion-modulated ionic conductor (AMIC) that enables in situ construction of electrolyte/electrode interphases for high-voltage SSLMBs by exploiting conformational transitions under multiple interactions between polymer and lithium salt anions. Anions modulate the decomposition behavior of supramolecular poly (vinylene carbonate) (PVC) at the electrode interface by changing the spatial conformation of the polymer chains, which further enhances ion transport and stabilizes the interfacial morphology. In addition, the AMIC weakens the "Li+-solvation" and increases Li+ vehicle sites, thereby enhancing the lithium-ion transport number (tLi +=~0.67). Consequently, Li || LiNi0.8Co0.1Mn0.1O2 cell maintains about 85 % capacity retention and Coulombic efficiency >99.8 % in 200 cycles at a charge cut-off voltage of 4.5 V. This study provides a new understanding of lithium salt anions regulating polymer chain segment behavior in the solid-state polymer electrolyte (SPE) and highlights the importance of the ion environment in the construction of interfacial phases and ionic conduction.

Electrified Interactions of Polyzwitterions with Charged Surfaces: Role of Dipole Orientation and Surface Potentials.

The zwitterionic groups possess strong dipole moments, leading to inter- or intrachain interactions among zwitterionic polymers. This study aims to demonstrate the interaction of polyzwitterions poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC), and poly(carboxybetaine methacrylate) (PCBMA) with electrified surfaces, despite their electrically neutral nature. We studied the adsorption of polyzwitterions and their monomers on electrified surfaces by using an electrochemical quartz crystal microbalance with dissipation (EQCM-D). The interaction between zwitterionic molecules and charged surfaces is explored by adjusting the surface potentials. Interestingly, the adsorption of polyzwitterions can be influenced by external potential, primarily due to the formation of polyzwitterions restricting the mobility of zwitterionic groups, affecting the adsorption behavior of polyzwitterions based on the surface potential. The impact is determined by the arrangement of positive and negative ions within the zwitterionic groups, which are the dipole orientation. Additionally, surface potentials determine the adsorption rate, amount, and chain conformation of the adsorbed thin polyzwitterion layers. The effect of ionic strength was investigated by introducing electrolytes into the aqueous solutions to assess the range of influenced surface potentials.

Meta-aramid film with both flexibility and strength: Combined effect of aromatic ether bond and micro-branched structure

Developing Meta-aramid materials that combine flexibility and strength will greatly expand their application fields. In previous work, it was demonstrated that aromatic ether bonds can contribute to improving flexibility. In addition, micro-branched chain structures can reduce intermolecular forces by increasing fractional free volume, while newly formed hydrogen bonding can maintain polymer strength. Therefore, two flexible polymers were obtained by incorporating 4,4′-diaminodiphenyl ether (ODA) and 4,4′-oxybis [3-(trifluoromethyl)benzenamine] (OTB) to the molecular chains, respectively, and flexible films were prepared by a combination of solution casting and dry-wet processing methods. By studying the properties of copolymer films with 10% ODA and 10% OTB added, it was found that they can maintain thermal stability and mechanical strength while improving the flexibility of the films. The AFM results visually showed that the DMT modulus of the modified films decreased at the micro level and DMA indicated that the introduction of ODA and OTB can shorten the molecular relaxation time, which reflected the improvement of molecular chain flexibility. Through molecular dynamics simulations, the differences were compared in molecular chain conformation, mean square displacement and hydrogen bonding after the introduction of ODA and OTB and the combined mechanism of aromatic ether bonds and CF3 side groups was confirmed in improving flexibility and maintaining mechanical strength.

The propensity for covalent organic frameworks to template polymer entanglement.

The introduction of molecularly woven three-dimensional (3D) covalent organic framework (COF) crystals into polymers of varying types invokes different forms of contact between filler and polymer. Whereas the combination of woven COFs with amorphous and brittle polymethyl methacrylate results in surface interactions, the use of the liquid-crystalline polymer polyimide induces the formation of polymer-COF junctions. These junctions are generated by the threading of polymer chains through the pores of the nanocrystals, thus allowing for spatial arrangement of polymer strands. This offers a programmable pathway for unthreading polymer strands under stress and leads to the in situ formation of high-aspect-ratio nanofibrils, which dissipate energy during the fracture. Polymer-COF junctions also strengthen the filler-matrix interfaces and lower the percolation thresholds of the composites, enhancing strength, ductility, and toughness of the composites by adding small amounts (~1 weight %) of woven COF nanocrystals. The ability of the polymer strands to closely interact with the woven framework is highlighted as the main parameter to forming these junctions, thus affecting polymer chain penetration and conformation.

Footprints of loop extrusion in statistics of intra-chromosomal distances: An analytically solvable model.

Active loop extrusion-the process of formation of dynamically growing chromatin loops due to the motor activity of DNA-binding protein complexes-is a firmly established mechanism responsible for chromatin spatial organization at different stages of a cell cycle in eukaryotes and bacteria. The theoretical insight into the effect of loop extrusion on the experimentally measured statistics of chromatin conformation can be gained with an appropriately chosen polymer model. Here, we consider the simplest analytically solvable model of an interphase chromosome, which is treated as an ideal chain with disorder of sufficiently sparse random loops whose conformations are sampled from the equilibrium ensemble. This framework allows us to arrive at the closed-form analytical expression for the mean-squared distance between pairs of genomic loci, which is valid beyond the one-loop approximation in diagrammatic representation. In addition, we analyze the loop-induced deviation of chain conformations from the Gaussian statistics by calculating kurtosis of probability density of the pairwise separation vector. The presented results suggest the possible ways of estimating the characteristics of the loop extrusion process based on the experimental data on the scale-dependent statistics of intra-chromosomal pair-wise distances.

Depth-profiling alkyl chain order in unsaturated lipid monolayers on water.

Unsaturated lipids with C=C groups in their alkyl chains are widely present in the cell membrane and food. The C=C groups alter the lipid packing density, membrane stability, and persistence against lipid oxidation. Yet, molecular-level insights into the structure of the unsaturated lipids remain scarce. Here, we probe the molecular structure and organization of monolayers of unsaturated lipids on the water surface using heterodyne-detected sum-frequency generation (HD-SFG) spectroscopy. We vary the location of the C=C in the alkyl chain and find that at high lipid density, the location of the C=C group affects neither the interfacial water organization nor the tail of the alkyl chain. Based on this observation, we use the C=C stretch HD-SFG response to depth-profile the alkyl chain conformation of the unsaturated lipid. We find that the first 1/3 of carbon atoms from the headgroup are relatively rigid, oriented perpendicular to the surface. In contrast, the remaining carbon atoms can be approximated as free rotators, introducing the disordering of the alkyl chains.

Poly(styrene-co-1-octene) behavioral differences in aliphatic and aromatic solvents: molecular dynamics simulation and DFT-D quantum calculations

Copolymerizing aromatic and aliphatic comonomers helps to create efficient superabsorbents to remove oil from seawater. In this work, the best sequence of styrene and 1-octene at different 1-octene molar percentages (x) was found for poly(styrene-r−1-octene) (CP-x) using neural network potential. According to the calculated characteristics of CP-x using molecular dynamics simulation, increasing the x amount up to 6% in the chain aromatic structure caused the chain expansion by ∼ 20% and the reduction of its diffusion coefficient in n-heptane by ∼ 70%. The determined Helmholtz free energy via thermodynamic integration formula showed a decrease from −2762.7 to −3818.3 kcal mol−1 (∼ 38% reduction) and entropy changes illustrated an increase from 5.12 to 8.21 kcal mol−1.K (∼ 60% increase) indicating a partial conversion of the copolymer nature from aromatic to aliphatic with raising x. This issue led to a ∼ 15% enhancement in the interaction energy between the chain and solvent media meaning a better tendency to n-heptane and the increment of the interfacial density of the solvent molecules around the copolymer chain with higher x. The quantum calculations also proved that toluene with the chain styrene ring, and n-heptane with the chain 1-octene have created a parallel orientation, due to the charge transfer energy arising from an occupied C-H bonding orbital to an adjacent one. This phenomenon moved the electron density to the boundary area between them and changed the chain conformation in the media. Compression of the CP-x characteristics in n-heptane and toluene unmasked the contrariwise behaviors of the copolymer in aliphatic and aromatic solvents, except CP-4, which is the best candidate to use in the oil absorption from water surfaces. The performed theoretical investigation of the CP-x has revealed the hidden molecular insights into the copolymer chain which can help experimentalists reduce their trial and error to manufacture efficient supper oil absorbents.

Insights into formation and stability mechanism of V7-type short amylose-resveratrol complex using molecular dynamics simulation and molecular docking

Pre-formed V-type amylose as a kind of wall material has been reported to carry polyphenols, while the interaction mechanism between V-type amylose and polyphenol is still elusive. In this work, the formation and stability mechanism of a V7-type short amylose-resveratrol complex was investigated via isothermal titration calorimetry, molecular dynamics, and molecular docking. The results presented that two stoichiometric ratios of resveratrol to short amylose were calculated to 0.120 and 0.800, and the corresponding main driving force was hydrogen bonding and hydrophobic interaction, respectively. The folding and unfolding conformation of V7-type short amylose chains appeared alternately during the simulation. Resveratrol tended to be bound in the short amylose helix between 40 ns and 80 ns to form a more stable complex. Hydrogen bonds between resveratrol molecule and O6 at the 22nd glucose molecule/O2 at the 24th glucose molecules and hydrophobic interaction between resveratrol molecule and glucose molecules (19th, 20th, 21st and 23rd) could be found.

Investigation of rheological properties of extruded composites based on UHMWPE

The influence of the CO-4 stabilizer on the rheological properties of polymer composite materials based on UHMWPE has been studied. It has been shown that the addition of a CO-4 stabilizer to polymer matrices significantly affects the rheological properties of materials and their extrudability. There is a change in the conformations of macromolecular chains, the absence of dependence of the viscous component on the relaxation process of the dispersed system, an increase in the complex viscosity, which led to a deterioration in the processability of the material. Based on the Han curves, it is shown that the addition of a CO-4 stabilizer leads to a deterioration in the miscibility of mixtures, i.e., the phase separation of the components of the obtained samples increases.

Anion‐modulated Ion Conductor with Chain Conformational Transformation for stabilizing Interfacial Phase of High‐Voltage Lithium Metal Batteries

AbstractIn solid‐state lithium metal batteries (SSLMBs), the inhomogeneous electrolyte‐electrode interphase layer aggravates the interfacial stability, leading to discontinuous interfacial ion/charge transport and continuous degradation of the electrolyte. Herein, we constructed an anion‐modulated ionic conductor (AMIC) that enables in situ construction of electrolyte/electrode interphases for high‐voltage SSLMBs by exploiting conformational transitions under multiple interactions between polymer and lithium salt anions. Anions modulate the decomposition behavior of supramolecular poly (vinylene carbonate) (PVC) at the electrode interface by changing the spatial conformation of the polymer chains, which further enhances ion transport and stabilizes the interfacial morphology. In addition, the AMIC weakens the “Li+‐solvation” and increases Li+ vehicle sites, thereby enhancing the lithium‐ion transport number (tLi+=~0.67). Consequently, Li || LiNi0.8Co0.1Mn0.1O2 cell maintains about 85 % capacity retention and Coulombic efficiency &gt;99.8 % in 200 cycles at a charge cut‐off voltage of 4.5 V. This study provides a new understanding of lithium salt anions regulating polymer chain segment behavior in the solid‐state polymer electrolyte (SPE) and highlights the importance of the ion environment in the construction of interfacial phases and ionic conduction.

Structure of a novel form of phosphopantetheine adenylyltransferase from Klebsiella pneumoniae at 2.59Å resolution.

Phosphopantetheine adenylyltransferase (EC. 2.7.7.3, PPAT) catalyzes the penultimate step of the multistep reaction in the coenzyme A (CoA) biosynthesis pathway. In this step, an adenylyl group from adenosine triphosphate (ATP) is transferred to 4'-phosphopantetheine (PNS) yielding 3'-dephospho-coenzyme A (dpCoA) and pyrophosphate (PPi). PPAT from strain C3 of Klebsiella pneumoniae (KpPPAT) was cloned, expressed and purified. It was crystallized using 0.1M HEPES buffer and PEG10000 at pH 7.5. The crystals belonged to tetragonal space group P41212 with cell dimensions of a = b = 72.82Å and c = 200.37Å. The structure was determined using the molecular replacement method and refined to values of 0.208 and 0.255 for Rcryst and Rfree factors, respectively. The structure determination showed the presence of three crystallographically independent molecules A, B and C in the asymmetric unit. The molecules A and B are observed in the form of a dimer in the asymmetric unit while molecule C belongs to the second dimer whose partner is related by crystallographic twofold symmetry. The polypeptide chain of KpPPAT folds into a β/α structure. The conformations of the side chains of several residues in the substrate binding site in KpPPAT are significantly different from those reported in other PPATs. As a result, the modes of binding of substrates, phosphopantetheine (PNS) and adenosine triphosphate (ATP) differ considerably. The binding studies using fluorescence spectroscopy indicated a KD value of 3.45 × 10-4M for ATP which is significantly lower than the corresponding values reported for PPAT from other species.

A comparison study on polysaccharides extracted from banana flower using different methods: Physicochemical characterization, and antioxidant and antihyperglycemic activities

This work investigated and compared the physicochemical characteristics, and antioxidant and antihyperglycemic properties in vitro of polysaccharides from a single banana flower variety (BFPs) extracted by different methods. BFPs extracted using hot water (HWE), acidic (CAE), alkaline (AAE), enzymatic (EAE), ultrasonic (UAE) and hot water-alkaline (HAE) methods showed different chemical composition, monosaccharide composition, molecular weight, chain conformation and surface morphology, but similar infrared spectra characteristic, main glycosidic residues, crystalline internal and thermal stability, suggesting that six methods have diverse impacts on the degradation of BFPs without changing the main structure. Then, among six BFPs, the stronger antioxidant activity in vitro was found in BFP extracted by HAE, which was attributed to its maximum uronic acid content (21.67 %) and phenolic content (0.73 %), and moderate molecular weight (158.48 kDa). The highest arabinose and guluronic acid contents (18.59 % and 1.31 % in molar ratios, respectively) and the lowest uronic acid content (14.30 %) in BFP extracted by HWE contributed to its better α-glucosidase inhibitory activity in vitro (66.55 %). The data offered theoretical evidence for choosing suitable extraction methods to acquire BFPs with targeted biological activities for applications, in which HAE and HWE could serve as beneficial methods for preparing antioxidant BFP and antihyperglycemic BFP, respectively.

Coupling relationship between molecule structure at silica/silicone gel interfaces and ionic conductivity in polymer composites

Herein, the coupling relationship between molecule structure and ion conductivity in silica filled silicone gel are established. Based on the broadband dielectric spectrum, the concentration of ion charges and ions diffusion coefficients, two key roles for ion conductivity, are calculated. The concentration of ion charges is increased by about four orders of magnitude after the addition of silica. Because of the more short-length chains conformations and more amorphous regions at interfaces, the chains at interfaces are easier to rearrange with higher relaxation frequency, which enhances the ions diffusion process and contributes to negative decoupling exponents between the interface molecule relaxations and ion diffusion coefficients in silicone gel composites. With the increase of fumed silica loading, the ionic conductivity increases first and decreases owing to percolation phenomenon about silica dispersion. Meanwhile, decoupling exponents of the interface molecules are closer to 0. Our findings deepen the understanding how the interface structures act on ions conductivity in insulating polymer composites, which is critical to rationally design interface structures for manipulating the insulation performances.

On the Swelling of Polymer Network Strands.

Large scale computer simulations are employed to analyze the conformations of network strands in polymer networks at preparation conditions (characterized by a polymer volume fraction of ϕ0) and when swollen to equilibrium (characterized by a polymer volume fraction ϕ < ϕ0). Network strands in end-linked model networks are weakly stretched and partially swollen at preparation conditions as compared to linear polymers in the same solvent at ϕ0. Equilibrium swelling causes non-ideal chain conformations characterized by an effective scaling exponent approaching 7/10 on intermediate length scales for increasing overlap of the chains. The chain size in a network consists of a fluctuating and a time average "elastic" contribution. The elastic contribution swells essentially affinely ∝(ϕ0/ϕ)2/3, whereas the swelling of the fluctuating part lies between the expected swelling of the entanglement constraints and the swelling of non-cross-linked chains in a comparable semi-dilute solution. The total swelling of chain size results from the changes of both fluctuating and non-fluctuatingcontributions.