Relative effects of polymer composition and sample preparation on glass dynamics.

Modern design of common adhesives, composites and polymeric parts makes use of polymer glasses that are stiff enough to maintain their shape under a high stress while still having a ductile behavior after the yield point. Typically, material compositions are tuned with co-monomers, polymer blends, plasticizers, or other additives to arrive at a tradeoff between the elastic modulus and toughness. In contrast, strong changes to the mechanics of a glass are possible by changing only the molecular packing during vitrification or even deep in the glassy state. For example, physical aging or processing techniques such as physical vapor deposition increase the density, embrittle the material, and increase elastic modulus. Here, we use molecular simulations, validated by positron annihilation lifetime spectroscopy (PALS) and quasi-elastic neutron scattering, to understand the free volume distribution and the resulting dynamics of glassy co-polymers where the composition is systemically varied between polar 5-norbornene-2-methanol (NBOH) and non-polar ethylidene norbornene (ENB) monomers. In these polymer glasses, we analyze the structural features of the unoccupied volume using clustering analysis, where the clustering is parameterized to reproduce experimental measurements of the same features from PALS. Further, we analyze the dynamics, quantified by the Debye-Waller factor, and compare the results with softer, lower density states. Our findings indicate that faster structural relaxations and potentially improved ductility are possible through changes to the geometric structure and fraction of the free volume, and that the resulting changes to the glass dynamics are comparable to large changes in the monomer composition.

Predicting Solute Diffusivity in Polymers Using Time-Temperature Superposition.

We demonstrate a novel application of the time-temperature superposition (TTS) principle to predict solute diffusivity D in glassy polymers using atomistic molecular dynamics simulations. Our TTS approach incorporates the Debye-Waller factor ⟨u2⟩, a measure of solute caging, along with concepts from thermodynamic scaling methods, allowing us to balance contributions to the dynamics from temperature and ⟨u2⟩ using adjustable parameters. Our approach rescales the solute mean-squared displacement curves at several temperatures into a master curve that approximates the diffusive dynamics at a reference temperature, effectively extending the simulation time scale from nanoseconds to seconds and beyond. With a set of "universal" parameters, this TTS approach predicts D with reasonable accuracy in a broad range of polymer/solute systems. Using TTS greatly reduces the computational cost compared to standard MD simulations. Thus, our method offers a means to rapidly and routinely provide order-of-magnitude estimates of D using simulations.

Relations Between Dynamic Localization and Solute Diffusion in Polymers.

Various public health concerns can arise from the unintended leaching of additives and impurities from polymeric medical devices or food packaging, which is directly related to each solute's diffusivity D. Both experimental and simulation methods can be used to quantify D, but slow diffusion at physiologic temperature in glassy polymers can render these approaches impractical. Here, we investigate a simulation approach with the potential to more rapidly calculate D. Specifically, we examine links between dynamic localization, characterized by the Debye-Waller factor, ⟨u2⟩, and D in a variety of polymer/solute systems using atomistic molecular dynamics (MD) simulations. Using short, high-temperature MD simulations to estimate D at physiologic temperature, we find that the relation ln D ∝ 1/⟨u2⟩ quantitatively predicts D for small solutes and produces an upper-bound estimate of D for larger solutes. Upper-bound estimates are useful in certain contexts, and we compare our results with another approach for determining upper bounds, the Piringer model, to show where each method may be useful. Then, we examine a modified relation where the Debye-Waller factor is rescaled by the mode coupling temperature Tc, which can produce better estimates of D if Tc is carefully chosen. Last, we compare our approach with several other models that relate temperature or localized dynamics with diffusivity. Although each of these approaches can be used to model D across wide temperature ranges using one or more adjustable parameters, none of them are truly predictive in glassy polymers. Further developments are needed to predict the optimal values of the adjustable parameters a priori.

Leveraging Extraction Testing to Predict Patient Exposure to Polymeric Medical Device Leachables Using Physics-based Models.

Toxicological risk assessment approaches are increasingly being used in lieu of animal testing to address toxicological concerns associated with release of chemical constituents from polymeric medical device components. These approaches currently rely on in vitro extraction testing in aggressive environments to estimate patient exposure to these constituents, but the clinical relevance of the test results is often ambiguous. Physics-based mass transport models can provide a framework to interpret extraction test results to provide more clinically relevant exposure estimates. However, the models require system-specific material properties, such as diffusion (D) and partition coefficients (K), to be established a priori for the extraction conditions. Using systems comprised high-density polyethylene and 4 different additives, we demonstrate that these properties can be quantified through standard extraction testing in hexane and isopropyl alcohol. The values of D and K derived in this manner were consistent with theoretical predictions for these quantities. Based on these results, we discuss both the challenges and benefits to leveraging extraction data to parameterize physics-based exposure models. Our observations suggest that clinically relevant, yet still conservative, exposure dose estimates provided by applying this approach to a single extraction measurement can be more than 100 times lower than would be measured under typical aggressive extraction conditions. However, to apply the framework on a routine basis, limiting values of D and K must be established for device-relevant systems either through the aggregation and analysis of more extensive extraction test data and/or advancements in theoretical and computational modeling efforts to predict these quantities.

Identifying Nonaffine Softening Modes in Glassy Polymer Networks: A Pathway to Chemical Design.

Using molecular simulations and theory, we develop an explicit mapping of the contribution of molecular relaxation modes in glassy thermosets to the shear modulus, where the relaxations were tuned by altering the polarity of side groups. Specifically, motions at the domain, segmental, monomer, and atomic levels are taken from molecular dynamics snapshots and directly linked with the viscoelasticity through a framework based in the lattice dynamics of amorphous solids. This unique approach provides direct insight into the roles of chemical groups in the stress response, including the time scale and spatial extent of relaxations during mechanics. Two thermoset networks with differing concentrations of polar side groups were examined, dicyclopentadiene (DCPD) and 5-norbornene-2-methanol (NBOH). A machine learning method is found to be effective for quantifying large-scale correlated motions, while more local chemical relaxations are readily identified by direct inspection. The approach is broadly applicable and enables rapid predictions of the frequency-dependent modulus for any glass.

Mechanics and nanovoid nucleation dynamics: effects of polar functionality in glassy polymer networks.

We use molecular simulations and experiments to rationalize the properties of a class of networks based on dicyclopentadiene (DCPD), a polymer with excellent fracture toughness and a high glass transition temperature (Tg), copolymerized with 5-norbornene-2-methanol (NBOH). DCPD is a highly non-polar hydrocarbon, while NBOH contains a hydroxy group, introducing polar functionality and hydrogen bonds (H-bonds). NBOH thus represents a possible route to improve the chemical compatibility of DCPD-based networks with less-hydrophobic materials. We systematically vary the NBOH content (polar chemistry) in DCPD networks, while keeping other network parameters nearly constant, including the molecular weight between cross-links, chain rigidity, and Tg. Using molecular dynamics (MD) simulations, we quantify the thermovolumetric and mechanical properties, including Tg, cohesive energy density, stiffness, and yield strength. We compare these results with experiments on networks of similar composition, finding good agreement. The relation between these properties and polar chemistry are studied by examining a secondary network of physical cross-links, formed by hydrogen bonds between NBOH units. Further, we examine nanovoid formation, an energy dissipation mechanism hypothesized to contribute to the toughness of pDCPD. Using metadynamics to accelerate sampling, we quantify the nanovoid nucleation rate under hydrostatic tension, similar to the stress state in the plastic zone preceding a crack tip. Small additions of NBOH have minimal effect, but the rate drops steeply with larger amounts. Several properties are mapped at nanometer scales, including stiffness and mobility, and associated with void nucleation. Estimates of the length- and time-scale of the plastic zone near a crack tip are used in discussing nanovoid formation as a plausible toughening mechanism in these materials. Overall, the results suggest that pDCPD tolerates the addition of some polar chemistry without degrading its excellent mechanical properties.

Parameter-free predictions of the viscoelastic response of glassy polymers from non-affine lattice dynamics.

We study the viscoelastic response of amorphous polymers using theory and simulations. By accounting for internal stresses and considering instantaneous normal modes (INMs) within athermal non-affine theory, we make parameter-free predictions of the dynamic viscoelastic moduli obtained in coarse-grained simulations of polymer glasses at non-zero temperatures. The theoretical results show very good correspondence with rheology data collected from molecular dynamics simulations over five orders of magnitude in frequency, with some instabilities that accumulate in the low-frequency part on approach to the glass transition. These results provide evidence that the mechanical glass transition itself is continuous and thus represents a crossover rather than a true phase transition. The relatively sharp drop of the low-frequency storage modulus across the glass transition temperature can be explained mechanistically within the proposed theory: the proliferation of low-eigenfrequency vibrational excitations (boson peak and nearly-zero energy excitations) is directly responsible for the rapid growth of a negative non-affine contribution to the storage modulus.

Influence of molecular weight between crosslinks on the mechanical properties of polymers formed via ring-opening metathesis.

The apparent molecular weight between crosslinks (Mc,a) in a polymer network plays a fundamental role in the network mechanical response. We systematically varied Mc,a independent of strong noncovalent bonding by using ring-opening metathesis polymerization (ROMP) to co-polymerize dicyclopentadiene (DCPD) with a chain extender that increases Mc,a or a di-functional crosslinker that decreases Mc,a. We compared the ROMP series quasi-static modulus (E), tensile yield stress (σy), and fracture toughness (KIC and GIC) in the glassy regime with literature data for more polar thermosets. ROMP resins showed high KIC (>1.5 MPa m0.5), high GIC (>1000 J m-2), and 4-5 times higher high rate impact resistance than typical polar thermosets with similar Tg values (100 °C to 178 °C). The overall E values were lower for ROMP systems. The σy dependence on Mc,a and T-Tg for ROMP resins was qualitatively similar to more polar thermosets, but the overall σy values were lower. In contrast to more polar thermosets, the KIC and GIC values of the ROMP resins showed strong Mc,a and T-Tg dependence. High rate impact (∼104-105 s-1) trends were similar to the KIC and GIC behavior, but were also correlated to σy. Overall, a ductile failure mode was observed for quasi-static and high rate results for a linear ROMP polymer (Mc,a = 1506 g mol-1 due to chain entanglement), and this gradually transitioned to a fully brittle failure mode for highly crosslinked ROMP polymers (Mc,a ≤ 270 g mol-1). Molecular dynamics (MD) simulations showed that low Mc,a ROMP resins were more likely to form molecular scale nanovoids. The higher chain stiffness in low Mc,a ROMP resins inhibited stress relaxation in the vicinity of these nanovoids, which correlated with brittle mechanical responses. Overall, these differences in mechanical properties were attributed to the weak non-covalent interactions in ROMP resins.

Topological structure and mechanics of glassy polymer networks.

The influence of chain-level network architecture (i.e., topology) on mechanics was explored for unentangled polymer networks using a blend of coarse-grained molecular simulations and graph-theoretic concepts. A simple extension of the Watts-Strogatz model is proposed to control the graph properties of the network such that the corresponding physical properties can be studied with simulations. The architecture of polymer networks assembled with a dynamic curing approach were compared with the extended Watts-Strogatz model, and found to agree surprisingly well. The final cured structures of the dynamically-assembled networks were nearly an intermediate between lattice and random connections due to restrictions imposed by the finite length of the chains. Further, the uni-axial stress response, character of the bond breaking, and non-affine displacements of fully-cured glassy networks were analyzed as a function of the degree of disorder in the network architecture. It is shown that the architecture strongly affects the network stability, flow stress, onset of bond breaking, and ultimate stress while leaving the modulus and yield point nearly unchanged. The results show that internal restrictions imposed by the network architecture alter the chain-level response through changes to the crosslink dynamics in the flow regime and through the degree of coordinated chain failure at the ultimate stress. The properties considered here are shown to be sensitive to even incremental changes to the architecture and, therefore, the overall network architecture, beyond simple defects, is predicted to be a meaningful physical parameter in the mechanics of glassy polymer networks.

Nanovoid formation and mechanics: a comparison of poly(dicyclopentadiene) and epoxy networks from molecular dynamics simulations.

Protective equipment in civilian and military applications requires the use of polymer materials that are both stiff and tough over a wide range of strain rates. However, typical structural materials, like tightly cross-linked epoxies, are very brittle. Recent experiments demonstrated that cross-linked poly(dicyclopentadiene) (pDCPD) networks can circumvent this trade-off by providing structural properties such as a high glass transition temperature and glassy modulus, while simultaneously exhibiting excellent toughness and high-rate impact resistance. The greater performance of pDCPD was attributed to more facile plastic deformation and nano-scale void formation, but the chemical and structural mechanisms underlying this response were not clear. Here, we use atomistic molecular dynamics to compare the molecular- and chain-level properties of pDCPD and epoxy networks undergoing high strain rate deformation. We quantify the tensile modulus and yield strength of the networks as well as the prevalence and characteristics of nanovoids that form during deformation. Networks of similar molecular weight between cross-links are compared. Two key molecular-level properties are identified - monomer flexibility and polar chemistry - that influence the behavior of the networks. Increasing monomer flexibility reduces the modulus and yield strength, while strong non-covalent interactions (e.g., hydrogen bonds) that accompany polar moieties provide higher modulus and yield strength. The lack of strong non-covalent interactions in pDCPD was found to account for its lower modulus and yield strength compared to the epoxies. We examine the molecular-level properties of nanovoids, such as shape, alignment, and local stress distribution, as well as the local chemical environment, finding that nanovoid formation and growth are increased by the monomer rigidity but decreased by polar chemistry. As a result, the pDCPD network, which has a stiff chain backbone with nonpolar alkane chemistry, exhibits more and larger nanovoids that grow more readily during deformation, which could account for the higher toughness and more ductile behavior observed in pDCPD.

Effect of Hydrophobic and Hydrophilic Surfaces on the Stability of Double-Stranded DNA.

DNA hybridization is the foundation for numerous technologies like DNA origami and DNA sensing/microarrays. Using molecular simulations, enhanced-sampling methods, and free-energy calculations, we show the effects of hydrophilic and hydrophobic surfaces on DNA hybridization. Hydrophilic surfaces compete with terminal bases' H-bonds but stabilize central base stacking. Hydrophobic surfaces strengthen terminal H-bonds but destabilize central base stacking. Regardless of surface chemistry, for terminal bases, melting proceeds through breaking H-bonds, followed by unstacking from the neighboring base. For central bases in bulk or near hydrophobic surfaces, melting proceeds by disruption of H-bonds, followed by unstacking, whereas on hydrophilic surfaces, unstacking from one neighboring base precedes complete disruption of the H-bonds, followed by unstacking from the second neighboring base. Kinetic barriers to melting and hybridization show that the central bases melt rapidly near hydrophobic surfaces, which can accelerate conformational searching and thereby accelerate folding into the desired conformation.

Interaction of hyaluronan binding peptides with glycosaminoglycans in poly(ethylene glycol) hydrogels.

This study investigates the incorporation of hyaluronan (HA) binding peptides into poly(ethylene glycol) (PEG) hydrogels as a mechanism to bind and retain hyaluronan for applications in tissue engineering. The specificity of the peptide sequence (native RYPISRPRKRC vs non-native RPSRPRIRYKC), the role of basic amino acids, and specificity to hyaluronan over other GAGs in contributing to the peptide-hyaluronan interaction were probed through experiments and simulations. Hydrogels containing the native or non-native peptide retained hyaluronan in a dose-dependent manner. Ionic interactions were the dominating mechanism. In diH2O the peptides interacted strongly with HA and chondroitin sulfate, but in phosphate buffered saline the peptides interacted more strongly with HA. For cartilage tissue engineering, chondrocyte-laden PEG hydrogels containing increasing amounts of HA binding peptide and exogenous HA had increased retention and decreased loss of cell-secreted proteoglycans in and from the hydrogel at 28 days. This new matrix-interactive hydrogel platform holds promise for tissue regeneration.

Molecular simulations of polycation-DNA binding exploring the effect of peptide chemistry and sequence in nuclear localization sequence based polycations.

Gene therapy relies on the delivery of DNA into cells, and polycations are one class of vectors enabling efficient DNA delivery. Nuclear localization sequences (NLS), cationic oligopeptides that target molecules for nuclear entry, can be incorporated into polycations to improve their gene delivery efficiency. We use simulations to study the effect of peptide chemistry and sequence on the DNA-binding behavior of NLS-grafted polycations by systematically mutating the residues in the grafts, which are based on the SV40 NLS (peptide sequence PKKKRKV). Replacing arginine (R) with lysine (K) reduces binding strength by eliminating arginine-DNA interactions, but placing R in a less hindered location (e.g., farther from the grafting point to the polycation backbone) has surprisingly little effect on polycation-DNA binding strength. Changing the positions of the hydrophobic proline (P) and valine (V) residues relative to the polycation backbone changes hydrophobic aggregation within the polycation and, consequently, changes the conformational entropy loss that occurs upon polycation-DNA binding. Since conformational entropy loss affects the free energy of binding, the positions of P and V in the grafts affect DNA binding affinity. The insight from this work guides synthesis of polycations with tailored DNA binding affinity and, in turn, efficient DNA delivery.

Sequence-specific recognition of cancer drug-DNA adducts by HMGB1a repair protein.

The efficacy of cancer drugs such as cisplatin (Cp) and oxaliplatin (Ox), which covalently bind to DNA to form drug-DNA adducts, is linked to their recognition by repair proteins such as HMGB1a. Previous experimental studies showed that HMGB1a's binding affinity for Cp- and Ox-DNA varies with the drug used and the local DNA sequence context of the adduct. We link this differential binding affinity to the free energy of deforming (bending and minor groove opening) the drug-DNA molecule during HMGB1a binding. Specifically, the minimal binding affinity of HMGB1a for Ox-DNA in the TGGA context is explained by its larger deformation free energy compared with Cp-DNA or Ox-DNA in other sequence contexts. Methyl groups on neighboring thymine bases in Ox-TGGA crowd the minor groove and sterically hinder the motion of the diaminocyclohexane ring of Ox, leading to this reduced deformability and resultant decrease in HMGB1a's binding affinity.

Understanding the effect of polylysine architecture on DNA binding using molecular dynamics simulations.

Polycations with varying chemistries and architectures have been synthesized and used in DNA transfection. In this paper we connect poly-L-lysine (PLL) architecture to DNA-binding strength, and in turn transfection efficiency, since experiments have shown that graft-type oligolysine architectures [e.g., poly(cyclooctene-g-oligolysine)] exhibit higher transfection efficiency than linear PLL. We use atomistic molecular dynamics simulations to study structural and thermodynamic effects of polycation-DNA binding for linear PLL and grafted oligolysines of varying graft lengths. Structurally, linear PLL binds in a concerted manner, while each oligolysine graft binds independently of its neighbors in the grafted architecture. Additionally, the presence of a hydrophobic backbone in the grafted architecture weakens binding to DNA compared to linear PLL. The binding free energy varies nonmonotonically with the graft length primarily due to entropic contributions. The binding free energy normalized to the number of bound amines is similar between the grafted and linear architectures at the largest (Poly5) and smallest (Poly2) graft length and stronger than the intermediate graft lengths (Poly3 and Poly4). These trends agree with experimental results that show higher transfection efficiency for Poly3 and Poly4 grafted oligolysines than for Poly5, Poly2, and linear PLL.