A Simple Generic Model of Elastin-Like Polypeptides with Proline Isomerization.

A generic model of elastin-like polypeptides (ELP) is derived that includes proline isomerization (ProI). As a case study, conformational transition of a -[valine-proline-glycine-valine-glycine]- sequence is investigated in aqueous ethanol mixtures. While the non-bonded interactions are based on the Lennard-Jones (LJ) parameters, the effect of ProI is incorporated by tuning the intramolecular 3- and 4-body interactions known from the underlying all-atom simulations into the generic model. One of the key advantages of such a minimalistic model is that it readily decouples the effects of geometry and the monomer-solvent interactions due to the presence of ProI, thus gives a clearer microscopic picture that is otherwise rather nontrivial within the all-atom setups. These results are consistent with the available all-atom and experimental data. The model derived here may pave the way to investigate large scale self-assembly of ELPs or biomimetic polymers in general.

Thermal Conductivity of Bottle-Brush Polymers.

Using molecular dynamics (MD) simulations of a generic model, we investigated heat propagation in bottle-brush polymers (BBP). An architecture is referred to as a BBP when a linear (backbone) polymer is grafted with the side chains of different length Ns and grafting density ρg, which control the bending stiffness of a backbone. Investigating κ-behavior in BBP is of particular interest due to two competing mechanics: increased backbone stiffness, via Ns and ρg, increases the thermal transport coefficient κ, while the presence of side chains provides additional pathways for heat leakage. We show how a delicate competition between these two effects controls κ. These results reveal that going from a weakly grafting (ρg < 1) to a highly grafting (ρg ≥ 1) regime, κ changes non-monotonically that is independent of Ns. The effect of side chain mass on κ and heat flow in the BBP melts is also discussed.

Smart Polymers for Soft Materials: From Solution Processing to Organic Solids.

Polymeric materials are ubiquitous in our everyday life, where they find a broad range of uses-spanning across common household items to advanced materials for modern technologies. In the context of the latter, so called "smart polymers" have received a lot of attention. These systems are soluble in water below their lower critical solution temperature Tℓ and often exhibit counterintuitive solvation behavior in mixed solvents. A polymer is known as smart-responsive when a slight change in external stimuli can significantly change its structure, functionm and stability. The interplay of different interactions, especially hydrogen bonds, can also be used for the design of lightweight high-performance organic solids with tunable properties. Here, a general scheme for establishing a structure-property relationship is a challenge using the conventional simulation techniques and also in standard experiments. From the theoretical side, a broad range of all-atom, multiscale, generic, and analytical techniques have been developed linking monomer level interaction details with macroscopic material properties. In this review, we briefly summarize the recent developments in the field of smart polymers, together with complementary experiments. For this purpose, we will specifically discuss the following: (1) the solution processing of responsive polymers and (2) their use in organic solids, with a goal to provide a microscopic understanding that may be used as a guiding tool for future experiments and/or simulations regarding designing advanced functional materials.

Stabilizing α-Helicity of a Polypeptide in Aqueous Urea: Dipole Orientation or Hydrogen Bonding?

We propose a mechanism for α-helix folding of polyalanine in aqueous urea that reconciles experimental and simulation studies. Over 15 µs long, all-atom simulations reveal that, upon dehydrating the protein's first solvation shell, a delicate balance between localized urea-residue dipole interactions and hydrogen bonds dictates polypeptide solvation properties and structure. Our work clarifies the experimentally observed tendency of these alanine-rich systems to form secondary structures at low and intermediate urea concentrations. Moreover, it is consistent with the commonly accepted hydrogen-bond-induced helix unfolding, dominant at high urea concentrations. These results establish a structure-property relationship highlighting the importance of microscopic dipole-dipole orientations/interactions for the operational understanding of macroscopic protein solvation.

Computational indentation in highly cross-linked polymer networks.

Indentation is a common experimental technique to study the mechanics of polymeric materials. The main advantage of using indentation is this provides a direct correlation between the microstructure and the small-scale mechanical response, which is otherwise difficult within the standard tensile testing. The majority of studies have investigated hydrogels, microgels, elastomers, and even soft biomaterials. However, a less investigated system is the indentation in highly cross-linked polymer (HCP) networks, where the complex network structure plays a key role in dictating their physical properties. In this work, we investigate the structure-property relationship in HCP networks using the computational indentation of a generic model. We establish a correlation between the local bond breaking, network rearrangement, and small-scale mechanics. The results are compared with the elastic-plastic deformation model. HCPs harden upon indentation.

Thermal Conductivity of Semicrystalline Polymer Networks: Crystallinity or Cross-Linking?

Understanding the heat flow in polymers is at the onset of many developments in designing advanced functional materials. Here, however, amorphous linear polymers usually exhibit a very low thermal conductivity κ, often hindering their broad applications. In this context, two common routes to increase κ are via semicrystallinity and cross-linking. It can therefore be inferred that the combination of these two effects may result in a further increase of κ with respect to the systems where only one of these two effects is important. Using molecular dynamics simulations, we investigate κ in semicrystalline polymer networks. Contrary to a priori understanding, we show that a combination of cross-linking and crystallinity does not always increase κ. Instead, a delicate competition between the lattice periodicity, the cross-linker types, and the bond density dictates the tunability of κ in these complex macromolecular systems. These results are also compared with the existing experiments.

Polymer cyclization for the emergence of hierarchical nanostructures.

The creation of synthetic polymer nanoobjects with well-defined hierarchical structures is important for a wide range of applications such as nanomaterial synthesis, catalysis, and therapeutics. Inspired by the programmability and precise three-dimensional architectures of biomolecules, here we demonstrate the strategy of fabricating controlled hierarchical structures through self-assembly of folded synthetic polymers. Linear poly(2-hydroxyethyl methacrylate) of different lengths are folded into cyclic polymers and their self-assembly into hierarchical structures is elucidated by various experimental techniques and molecular dynamics simulations. Based on their structural similarity, macrocyclic brush polymers with amphiphilic block side chains are synthesized, which can self-assemble into wormlike and higher-ordered structures. Our work points out the vital role of polymer folding in macromolecular self-assembly and establishes a versatile approach for constructing biomimetic hierarchical assemblies.

Thermal Transport in Molecular Forests.

Heat propagation in quasi-one-dimensional materials (Q1DMs) often appears puzzling. For example, while an isolated Q1DM, such as a nanowire, a carbon nanotube, or a polymer, can exhibit a high thermal conductivity κ, forests of the same materials can show a reduction in κ. Until now, the complex structures of these assemblies have hindered the emergence of a clear molecular picture for this intriguing phenomenon. We combine coarse-grained simulations with concepts known from polymer physics and thermal transport to unveil a generic microscopic picture of κ reduction in molecular forests. We show that a delicate balance among the persistence length of the Q1DM, the segment orientations, and the flexural vibrations governs the reduction in κ.

Why Do Elastin-Like Polypeptides Possibly Have Different Solvation Behaviors in Water-Ethanol and Water-Urea Mixtures?

The solvent quality determines the collapsed or the expanded state of a polymer. For example, a polymer dissolved in a poor solvent collapses, whereas in a good solvent it opens up. While this standard understanding is generally valid, there are examples when a polymer collapses even in a mixture of two good solvents. This phenomenon, commonly known as co-non-solvency, is usually associated with a wide range of synthetic (smart) polymers. Moreover, recent experiments have shown that some biopolymers, such as elastin-like polypeptides (ELPs) that exhibit lower critical solution behavior T l in pure water, show co-non-solvency behavior in aqueous ethanol mixtures. In this study, we investigate the phase behavior of elastin-like polypeptides (ELPs) in aqueous binary mixtures using molecular dynamics simulations of all-atom and complementary explicit solvent generic models. The model is parameterized by mapping the solvation free energy obtained from the all-atom simulations onto the generic interaction parameters. For this purpose, we derive segment-based (monomer level) generic parameters for four different peptides, namely proline (P), valine (V), glycine (G), and alanine (A), where the first three constitute the basic building blocks of ELPs. Here, we compare the conformational behavior of two ELP sequences, namely -(VPGGG)- and -(VPGVG)-, in aqueous ethanol and -urea mixtures. Consistent with recent experiments, we find that ELPs show co-non-solvency in aqueous ethanol mixtures. Ethanol molecules have preferential binding with all ELP residues, with an interaction contrast of 6-8 k B T, and thus driving the coil-to-globule transition. On the contrary, ELP conformations show a weak variation in aqueous urea mixtures. Our simulations suggest that the glycine residues dictate the overall behavior of ELPs in aqueous urea, where urea molecules have a rather weak preferential binding with glycine as observed from the all atom simulations, i.e., less than k B T. This weak interaction dilutes the overall effect of other neighboring residues and thus ELPs exhibit a different conformational behavior in aqueous urea in comparison to aqueous ethanol mixtures. While the validation of the latter findings will require a more detailed experimental investigation, the results presented here may provide a new twist to the present understanding of cosolvent interactions with peptides and proteins.

Precision Anisotropic Brush Polymers by Sequence Controlled Chemistry.

The programming of nanomaterials at molecular length-scales to control architecture and function represents a pinnacle in soft materials synthesis. Although elusive in synthetic materials, Nature has evolutionarily refined macromolecular synthesis with perfect atomic resolution across three-dimensional space that serves specific functions. We show that biomolecules, specifically proteins, provide an intrinsic macromolecular backbone for the construction of anisotropic brush polymers with monodisperse lengths via grafting-from strategy. Using human serum albumin as a model, its sequence was exploited to chemically transform a single cysteine, such that the expression of said functionality is asymmetrically placed along the backbone of the eventual brush polymer. This positional monofunctionalization strategy was connected with biotin-streptavidin interactions to demonstrate the capabilities for site-specific self-assembly to create higher ordered architectures. Supported by systematic experimental and computational studies, we envisioned that this macromolecular platform provides unique avenues and perspectives in macromolecular design for both nanoscience and biomedicine.

Studying polymer solutions with particle-based models linked to classical density functionals: co-non-solvency.

We demonstrate the potential of hybrid particle-based models, where interactions are introduced through functionals of local order parameters, in describing multicomponent polymer solutions. The link to a free-energy-like functional is advantageous for controlling the thermodynamics of the model. We focus on co-non-solvency - the collapse of polymer chains in dilute mixtures with two miscible good solvents, having different affinities towards the polymer. We employ a simple model where polymers and solvents are represented, respectively, by worm-like chains and single particles. Non-bonded interactions are captured by a polynomial which is third order in local densities and can, therefore, describe liquid-vapour coexistence. The parameterisation of the functional benefits from an elementary mean-field approximation to the statistical mechanics of the model. The model provides a framework for Monte Carlo simulations using a particle-to-mesh algorithm. Studies with conventional generic bead-spring and all-atom models have demonstrated that co-non-solvency is caused by preferential binding of the better solvent (termed cosolvent) with polymer. Hence, segmental loops bridged by cosolvent molecules are formed, initiating polymer collapse. The mesoscopic hybrid model differs conceptually from the conventional microscopic descriptions. Yet, it reproduces the same co-non-solvency mechanism supporting its universality. Films of adsorbed ternary solutions, showing co-non-solvency in the dilute regime, are considered at high concentrations. In this case, chains do not collapse. The properties of loops and tails of the adsorbed polymer agree with early theoretical predictions obtained for concentrated binary solutions.

Polyacrylamide "revisited": UCST-type reversible thermoresponsive properties in aqueous alcoholic solutions.

Combining experiments and all-atom molecular dynamics simulations, we study the conformational behavior of polyacrylamide (PAM) in aqueous alcohol mixtures over a wide range of temperatures. This study shows that even when the microscopic interaction is dictated by hydrogen bonding, unlike its counterparts that present a lower critical solution temperature (LCST), PAM shows a counterintuitive tunable upper critical solution temperature (UCST)-type phase transition in water/alcohol mixtures that was not reported before. The phase transition temperature was found to be tunable between 4 and 60 °C by the type and concentration of alcohol in the mixture as well as by the solution concentration and molecular weight of the polymer. In addition, molecular dynamics simulations confirmed a UCST-like behaviour of the PAM in aqueous alcoholic solutions. Additionally, it was observed that the PAM is more swollen in pure alcohol solutions than in 80% alcoholic solutions due to θ-like behaviour. Additionally, in the globular state, the size of the aggregates was found to increase with increasing solvent hydrophobicity and polymer concentration of the solutions. Above its phase transition temperature, PAM might be present as individual polymer chains in the coil state (≤10 nm). As PAM is a widespread polymer in many biomedical applications (gel electrophoresis, etc.), this finding could be of high relevance for many more practical applications in high performance pharmaceuticals and/or sensors.

Collapse in two good solvents, swelling in two poor solvents: defying the laws of polymer solubility?

In this work we discuss two mirror but distinct phenomena of polymer paradoxical properties in mixed solvents: co-non-solvency and co-solvency. When a polymer collapses in a mixture of two miscible good solvents the phenomenon is known as co-non-solvency, while co-solvency is a phenomenon that is associated with the swelling of a polymer in poor solvent mixtures. A typical example of co-non-solvency is provided by poly(N-isopropylacrylamide) in aqueous alcohol, while poly(methyl methacrylate) in aqueous alcohol shows co-solvency. We discuss these two phenomena to compare their microscopic origins and show that both can be understood within generic universal concepts. A broad range of polymers is therefore expected to exhibit these phenomena where specific chemical details play a lesser role than the appropriate combination of interactions between the trio of molecular components.

Depleted depletion drives polymer swelling in poor solvent mixtures.

Establishing a link between macromolecular conformation and microscopic interaction is a key to understand properties of polymer solutions and for designing technologically relevant "smart" polymers. Here, polymer solvation in solvent mixtures strike as paradoxical phenomena. For example, when adding polymers to a solvent, such that all particle interactions are repulsive, polymer chains can collapse due to increased monomer-solvent repulsion. This depletion induced monomer-monomer attraction is well known from colloidal stability. A typical example is poly(methyl methacrylate) (PMMA) in water or small alcohols. While polymer collapse in a single poor solvent is well understood, the observed polymer swelling in mixtures of two repulsive solvents is surprising. By combining simulations and theoretical concepts known from polymer physics and colloidal science, we unveil the microscopic, generic origin of this collapse-swelling-collapse behavior. We show that this phenomenon naturally emerges at constant pressure when an appropriate balance of entropically driven depletion interactions is achieved.

Reply to the 'Comment on "Relating side chain organization of PNIPAm with its conformation in aqueous methanol"' by A. Pica and G. Graziano, Soft Matter, 2017, 13, DOI: 10.1039/C7SM01065F.

We have recently proposed preferential binding by a cosolvent as the mechanism for chain collapse under co-non-solvency. Here we summarise our earlier works and provide further evidence that alcohol preferentially binds to PNIPAm, forming cosolvent bridges, and thus drives the transition. We also clarify some of the common misconceptions evoked in this debate with Pica and Graziano (PG), reinforcing the arguments of our earlier reply-comment [Soft Matter, 2017, 13, 2292] and published works.

Sequence transferable coarse-grained model of amphiphilic copolymers.

Polymer properties are inherently multi-scale in nature, where delicate local interaction details play a key role in describing their global conformational behavior. In this context, deriving coarse-grained (CG) multi-scale models for polymeric liquids is a non-trivial task. Further complexities arise when dealing with copolymer systems with varying microscopic sequences, especially when they are of amphiphilic nature. In this work, we derive a segment-based generic CG model for amphiphilic copolymers consisting of repeat units of hydrophobic (methylene) and hydrophilic (ethylene oxide) monomers. The system is a simulation analogue of polyacetal copolymers [S. Samanta et al., Macromolecules 49, 1858 (2016)]. The CG model is found to be transferable over a wide range of copolymer sequences and also to be consistent with existing experimental data.

Reply to the 'Comment on "Relating side chain organization of PNIPAm with its conformation in aqueous methanol"' by N. van der Vegt and F. Rodriguez-Ropero, Soft Matter, 2017, 13, DOI: 10.1039/C6SM02139E.

In a comment van der Vegt and Rodriguez-Ropero (vdVRR) challenged our explanation of the co-non-solvency effect of PNIPAm in aqueous methanol solutions. They argue, based on a careful selection of published studies including some of their own, that direct repulsions between the different constituents are sufficient to understand this phenomenon. According to vdVRR, the emerging view of entropic collapse, put forward by Flory (1910-1985) to explain common polymers in poor solvents, would be enough to explain co-non-solvency. In this reply we attempt to bring this discussion into firmer grounds. We provide a more comprehensive view of available experimental, numerical and theoretical results and review basic concepts of physical chemistry and of statistical mechanics of polymer collapse that show how methanol mediated attractions between chain monomers are required to understand this fascinating behavior.

Effects of stereochemistry and copolymerization on the LCST of PNIPAm.

Poly(N-isopropylacrylamide) (PNIPAm) is a smart polymer that presents a lower critical transition temperature (LCST) of 305 K. Interestingly, this transition point falls within the range of the human body temperature, making PNIPAm a highly suitable candidate for bio-medical applications. However, it is sometimes desirable to have a rather flexible tuning of the LCST of these polymers to further increase their range of applications. In this work, we use all-atom molecular dynamics simulations to study the LCST of PNIPAm-based (co-)polymers. We study different molecular architectures where the polymer sequences are tuned either by modifying its stereochemistry or by the co-polymerization of PNIPAm with acrylamide (Am) units. Our analysis connects global polymer conformations with the microscopic intermolecular interactions. These findings suggest that the collapse of a PNIPAm chain upon heating is dependent on the hydration structure around the monomers, which is strongly dependent on the tacticity and the presence of more hydrophilic acrylamide monomers. Our results are found to be in good agreement with the existing experimental data.

Synthesis of Peptide-Functionalized Poly(bis-sulfone) Copolymers Regulating HIV-1 Entry and Cancer Stem Cell Migration.

Peptide-polymer conjugates have been regarded as primary stronghold in biohybrid nanomedicine, which has seen extensive development due to its intrinsic property to provide complementary functions of both the peptide material and the synthetic polymer platform. Here we present an advanced macromolecular therapeutic that targets two exclusive classes of important diseases (namely, the HIV and cancer) that are implicated by extremely different causative agents. Using a facile thiol-reactive monomer, the eventual polymer facilitates multivalent conjugation of an endogenous peptide WSC02 that targets the CXCR4 chemokine receptor. The biohybrid material demonstrated both potent antiviral effects against HIV-1 as well as inhibiting cancer stem cell migration thus establishing the foundation for multimodal nanotherapeutics that simultaneously target more than one class of disease implications.

Poly(N-isopropylacrylamide) Microgels under Alcoholic Intoxication: When a LCST Polymer Shows Swelling with Increasing Temperature.

Poly(N-isopropylacrylamide) (PNIPAM) microgel is a smart polymer that shows a volume phase transition temperature (VPTT) at around 32 °C in aqueous solutions, above which it collapses. In this work, combining experiments and molecular simulations, it is shown that PNIPAM microgels do not always exhibit a collapsed structure above the VPTT. Instead, PNIPAM in aqueous alcohol mixtures shows a two-step conformational transition, i.e., a collapse at low temperatures (T < 32 °C) and a reswelling when T > 50 °C. The present analysis indicates that delicate microscopic interaction details, together with the bulk solution properties, play a key role in dictating the reswelling behavior. Even when PNIPAM microgels swell with increasing T, this is not a standard upper critical solution behavior.