Role of Dipeptide Terminal-End Association on the Structural, Dynamic, and Rheological Properties of Natural Rubber

The end-group chemistry of cis-1,4-polyisoprene (PI) chains is critical in governing the exceptional mechanical performance of Hevea natural rubber (NR). PI chains exhibit distinct terminal groups, classified into ω and α types. Experimental studies have identified two types of ω terminal ends and six α terminal ends (α1, ..., and α6). In this study, we investigate five polyisoprene melt systems, each with unique combinations of terminal groups: hydrogen (H), ω, ω′, α5, and α6. The ω end consists of a dimethyl-allyl group bonded to two trans-isoprene units, whereas the ω′ group consists of an alanine dipeptide (ADP) segment linked to a dimethyl-allyl and two trans-isoprene units. The α5 and α6 groups correspond to the ester and hydroxy terminal groups. The studied systems include hydrogen-terminated HPIH (PI0); ester-terminated ωPIα5 (PIV); hydroxy-terminated ωPIα6 (PIVI); and dipeptide-terminated ω′PIα5,α6 (PIV′,VI′). Using all-atom molecular dynamics simulations, we evaluated conformational properties, including the end-to-end distance, radius of gyration, Kuhn length, and dynamic (end-to-end vector autocorrelation, Rouse modes) properties. Intermolecular interactions were characterized using radial distribution functions and the corresponding potentials of mean force. Pronounced hydrogen bonding among ω′–ω′ and ω′–α groups leads to slower dynamics and the formation of stable clusters in ω′PIα5,α6 systems. These clusters act as physical junction points (PJPs) stabilized by β-sheet-like hydrogen-bond networks between dipeptide terminal ends. The stress–stress autocorrelation function, G(t), reveals a chain length-dependent slowdown in relaxation dynamics for (PI0,V) systems, with slower relaxation observed at N = 96 (N is the number of monomer present in each chain) compared to N = 24. In contrast, (PIV′,VI′) chains exhibit faster relaxation at N = 96, attributed to weakened end-group associations and the absence of large clusters that dominate the N = 24 systems. These findings demonstrate that β-sheet-like PJPs may be the key to the outstanding properties of NR.