Role of Terminal Groups of cis-1,4-Polyisoprene Chains in the Formation of Physical Junction Points in Natural Rubber

Molecular Defenders: Proteins and Phospholipids Enhancing Natural Rubber's Resilience

Natural rubber (NR), a cis-1,4-polyisoprene biopolymer, exhibits excellent mechanical strength and oxidative stability, partly due to the presence of nonrubber components (NRCs) such as proteins and phospholipids. However, the molecular mechanisms by which NRCs influence NR's performance remain poorly understood. In this study, molecular dynamics (MD) simulations and quantum mechanical (QM) calculations are combined to investigate the role of NRCs in enhancing the thermo-mechanical and oxidative stability of NR. MD simulations show that NRCs form strong hydrogen-bonding (H-bonding) networks, increasing the glass transition temperature (Tg), reducing chain mobility, and introducing physical cross-links that enhance mechanical integrity. QM calculations reveal that specific protein residues (e.g., Pro_H4) have low N-H bond dissociation energies (BDE = 158.61 kJ·mol-1), allowing efficient hydrogen atom transfer (HAT) to quench free radicals. The combined MD/QM results demonstrate a dual stabilization mechanism: NRC-functionalized model systems exhibit low oxygen permeability (P = 3.0 × 10 -9 cm2/s kPa at 298 K), which limits radical formation, while protein-based antioxidants actively scavenge radicals. This synergy between reduced oxygen transport and intrinsic radical quenching provides a molecular basis for the oxidative resistance of NR. These findings clarify the structural role of NRCs in NR and offer a design strategy for developing durable, bioinspired elastomers with built-in oxidative protection.

Comprehensive investigation of the interactions between natural rubber and lignin by molecular dynamics simulation

Currently, the interaction behavior of natural rubber-lignin (NR-L) remains unclear. In this study, we successfully replicated the density, glass transition temperature, and mechanical properties of NR-L using molecular dynamics coupled with GAFF. Using these models, we rigorously investigated the interaction behavior of these systems, which revealed that when the ambient temperature was lower than the thermal decomposition temperature, there was almost no impact on system properties, including density, structure, interaction forces, radial pair distribution function, free volume, radius of gyration, and lignin hydrogen bonding, as no significant enthalpy change occurred. The influence of hardwood lignin and softwood lignin on NR strength varied according to the concentration of lignin. At low concentration, the electron density cloud between highly branched hardwood lignin and NR is lower, leading to smaller interactions. However, at higher concentrations, the van der Waals term between the less polar and larger number of atoms of hardwood lignin and NR becomes stronger, resulting in the opposite trend being observed. Furthermore, NR-L is governed primarily by van der Waals forces, while lignin-lignin is governed primarily by electrostatic interactions. These detailed characterizations offered valuable insight for future research endeavors aimed at designing and synthesizing green NR-L composites at the atomic scale.

Exploring the Role of Hydroxy- and Phosphate-Terminated cis-1,4-Polyisoprene Chains in the Formation of Physical Junction Points in Natural Rubber: Insights from Molecular Dynamics Simulations

This study elucidates the pivotal role of terminal structures in cis-1,4-polyisoprene (PI) chains, contributing to the exceptional mechanical properties of Hevea natural rubber (NR). NR's unique networking structure, crucial for crack resistance, elasticity, and strain-induced crystallization, involves two terminal groups, ω and α. The proposed ω terminal structure is dimethyl allyl-(trans-1,4-isoprene)2, and α terminals exist in various forms, including hydroxy, ester, and phosphate groups. Among others, we investigated three types of cis-1,4-PI with different terminal combinations: HPIH (pure PI with H terminal), ωPIα6 (PI with ω and α6 terminals), and ωPIPO4 (PI with ω and PO4 terminals) and revealed significant dynamics variations. Hydrogen bonds between α6 and α6 and PO4 and PO4 residues in ωPIα6 and ωPIPO4 systems induce slower dynamics of hydroxy- and phosphate-terminated PI chains. Associations between α6 and α6 and PO4 and PO4 terminals are markedly stronger than ω and ω, and hydrogen terminals in HPIH and ω PIα6,PO4 systems. Phosphate terminals exhibit a stronger mutual association than hydroxy terminals. Potentials of mean force analysis and cluster-formation-fraction computations reveal stable clusters in ωPIα6 and ωPIPO4 , supporting the formation of polar aggregates (physical junction points). Notably, phosphate terminal groups facilitate large and highly stable phosphate polar aggregates, crucial for the natural networking structure responsible for NR's outstanding mechanical properties compared to synthetic PI rubber. This comprehensive investigation provides valuable insights into the role of terminal groups in cis-1,4-PI melt systems and their profound impact on the mechanical properties of NR.

In silico discovery of potential PPI inhibitors for anti-lung cancer activity by targeting the CCND1-CDK4 complex via the P21 inhibition mechanism

Non-Small Cell Lung Cancer (NSCLC) is a prevalent and deadly form of lung cancer worldwide with a low 5-year survival rate. Current treatments have limitations, particularly for advanced-stage patients. P21, a protein that inhibits the CCND1-CDK4 complex, plays a crucial role in cell proliferation. Computer-Aided Drug Design (CADD) based on pharmacophores can screen and design PPI inhibitors targeting the CCND1-CDK4 complex. By analyzing known inhibitors, key pharmacophores are identified, and computational methods are used to screen potential PPI inhibitors. Molecular docking, pharmacophore matching, and structure-activity relationship studies optimize the inhibitors. This approach accelerates the discovery of CCND1-CDK4 PPI inhibitors for NSCLC treatment. Molecular dynamics simulations of CCND1-CDK4-P21 and CCND1-CDK4 complexes showed stable behavior, comprehensive sampling, and P21's impact on complex stability and hydrogen bond formation. A pharmacophore model facilitated virtual screening, identifying compounds with favorable binding affinities. Further simulations confirmed the stability and interactions of selected compounds, including 513457. This study demonstrates the potential of CADD in optimizing PPI inhibitors targeting the CCND1-CDK4 complex for NSCLC treatment. Extended simulations and experimental validations are necessary to assess their efficacy and safety.

Ionic Pairing and Selective Solvation of Butylmethylimidazolium Chloride Ion Pairs in DMSO-Water Mixtures: A Comprehensive Examination via Molecular Dynamics Simulations and Potentials of Mean Force Analysis

Ionic liquids (ILs) with dimethyl sulfoxide (DMSO) and water act as a promising solvent medium for the dissolution of cellulose in an efficient manner. To develop a proper solvent system, it is really important to understand the thermodynamics of the molecular solutions consisting of ILs, DMSO, and water. The ion-pairing propensity of the ILs in the presence of DMSO and water plays a crucial role in governing the property of the solvent mixtures. Employing all-atom molecular dynamics simulations, we estimate the potentials of mean force between BMIM+ and Cl- ions in DMSO-water mixtures. Analysis reveals a significant increase in the thermodynamic stability of both contact ion pair (CIP) and solvent-assisted ion pair (SAIP) states with a rising DMSO mole fraction. Thermodynamic assessments highlight the entropic stabilization of CIP states and SAIP states in pure water, in DMSO-water mixtures, and in pure DMSO. The structural analysis reveals that in comparison to the DMSO local density, the local water density is relatively very high around ion pairs, more specifically in the solvation shell of a chloride ion. Preferential binding coefficients also consistently indicate exclusion of DMSO from the ion pair in DMSO-water mixtures. To enhance our understanding regarding the solvent molecules kinetics around the ion pairs, the survival probabilities of DMSO and water are computed. The calculations reveal that the water molecules prefer a prolonged stay in the solvation shell of Cl- ions.

Interactions between Water and a Hydrophobic Polymer

To investigate the mechanisms of interactions between a hydrophobic polymer and water, molecular dynamics calculations and Raman spectroscopic measurements of cis-1,4-polyisoprene (PI)-water systems were performed. The results show that PI in water undergoes a coil-globule transition at around 248 K. The transition is attributed to changes in the density and diffusivity of water. The volume expansion of the supercooled liquid water induces the coil structure of PI. The phase separation of PI from water with an increase in the self-diffusion coefficient of water molecules results in the globule structure of PI. The self-diffusion coefficient of free water with PI is larger than that of pure water because PI has an effect to decrease the hydrogen-bonding strength of water. The result suggests that the effects of the coexisting water are important factors governing the physical and chemical properties of hydrophobic polymers.

Strain hardening in biaxially stretched elastomers undergoing strain-induced crystallization

We reveal strain hardening due to strain-induced crystallization (SIC) in both cross-linked natural rubber (NR) and its synthetic analogue (IR) under planar extension, a type of biaxial stretching where the rubber is stretched in one direction while maintaining the dimension in the other direction unchanged. Utilizing a bespoke biaxial tensile tester, planar extension tests were conducted on geometrically designed and optimally shaped sheet specimens to achieve a uniform and highly strained field. Evident strain hardening due to SIC was observed in both stretching (x) and constrained (y) directions when the stretch (λx) exceeded a critical value λx,c. The λx,c value aligned with the onset stretch of SIC in planar extension, as determined by wide-angle X-ray scattering measurements. Interestingly, the nominal stress ratio between the constrained (σy) and stretching (σx) axes as a function of λx exhibited a distinct minimum near λx,c. This minimum signifies that the increment of σx induced by an increase in λx surpasses that of σy before strain hardening (λx < λx,c), while the relationship is reversed in the strain hardening region (λx > λx,c). The λx,c value in planar extension (4.7 for IR and 4.5 for NR) was slightly lower than that in uniaxial extension (5.7 for IR and 5.2 for NR). This difference in λx,c values can be explained by considering a single mechanical work required for strain hardening, owing to the relatively small dissimilarities between the two stretching modes. This investigation contributes significantly to the understanding of SIC phenomena in biaxial stretching, and provides valuable insights for predicting the mechanical response of SIC rubber under various deformation conditions.