All-atom molecular dynamics simulation of solvent diffusion in an unentangled polystyrene film.

The diffusion behavior of low molecular weight solvents within an unentangled polystyrene film below and above its glass transition temperature is investigated. The diffusion behavior in the glassy state exhibits a distinct behavior known as case II or class II diffusion, noticeably diverging from conventional Fickian diffusion observed above the glass transition temperature of the polymer film. In the context of case II diffusion, the primary experimental observation entails the emergence of a well-defined concentration front moving at a constant speed, delineating a swollen, rubbery region from a glassy region within the polymer system. Despite the prevalence of this phenomenon in experimental settings, simulating case II diffusion has posed a significant challenge, primarily due to the computationally intensive nature of the diffusion process. To address this, we have developed an all-atom molecular dynamics simulation approach for the observation of case II diffusion in glassy polymers. This method aims to unravel the intricacies of the diffusion process, providing valuable insights into the dynamic interactions between solvents and the polymer matrix.

Elucidation of Dithiol-yne Comb Polymer Architectures by Tandem Mass Spectrometry and Ion Mobility Techniques.

Polymers have a wide range of applications depending on their composition, size, and architecture. Varying any of these three characteristics can greatly impact the resulting chemical, physical, and mechanical properties. While many techniques are available to determine polymer composition and size, determining the exact polymer architecture is more challenging. Herein, tandem mass spectrometry (MS/MS) and ion mobility mass spectrometry (IM-MS) methods are utilized to derive crucial architectural information about dithiol-yne comb polymers. Based on their unique fragmentation products and IM drift times, dithiol-yne oligomers with distinct architectures were successfully differentiated and characterized. Additionally, experimental collision cross-sections (Ω) derived via IM-MS were compared to theoretically extracted Ω values from molecular dynamics simulated structures to deduce the architectural motif of these comb oligomers. Overall, this work demonstrates the benefits of combining various mass spectrometry techniques in order to gain a complete understanding of a complex polymer mixture.

Comment on "Effects of topological constraints on linked ring polymers in solvents of varying quality" by Z. A. Dehaghani, I. Chubak, C. N. Likos and M. R. Ejtehadi, Soft Matter, 2020, 16, 3029.

This comment critically evaluates the work of Dehaghani et al., who investigated the conformational behavior of catenated polymers under diverse solvent conditions using coarse-grained molecular dynamics simulations. While their study provides valuable insights into the scaling behavior of poly[n]catenane's radius of gyration in a good solvent, significant discrepancies arise, particularly concerning the reported θ-temperature trends. The validity of their methodology in determining θ-temperatures for linear and ring polymers is questioned, given observed disparities in chosen number of bead ranges that imply varying molecular weights. This comment underscores the need for a meticulous reassessment of the methodologies and interpretations presented in Dehaghani et al.'s study, emphasizing the importance of rigorous considerations in the investigation of the physical properties of catenated polymers.

Synergistic Effect of Physical and Chemical Cross-Linkers Enhances Shape Fidelity and Mechanical Properties of 3D Printable Low-Modulus Polyesters.

Three-dimensional (3D) printing is becoming increasingly prevalent in tissue engineering, driving the demand for low-modulus, high-performance, biodegradable, and biocompatible polymers. Extrusion-based direct-write (EDW) 3D printing enables printing and customization of low-modulus materials, ranging from cell-free printing to cell-laden bioinks that closely resemble natural tissue. While EDW holds promise, the requirement for soft materials with excellent printability and shape fidelity postprinting remains unmet. The development of new synthetic materials for 3D printing applications has been relatively slow, and only a small polymer library is available for tissue engineering applications. Furthermore, most of these polymers require high temperature (FDM) or additives and solvents (DLP/SLA) to enable printability. In this study, we present low-modulus 3D printable polyester inks that enable low-temperature printing without the need for solvents or additives. To maintain shape fidelity, we incorporate physical and chemical cross-linkers. These 3D printable polyester inks contain pendant amide groups as the physical cross-linker and coumarin pendant groups as the photochemical cross-linker. Molecular dynamics simulations further confirm the presence of physical interactions between different pendants, including hydrogen bonding and hydrophobic interactions. The combination of the two types of cross-linkers enhances the zero-shear viscosity and hence provides good printability and shape fidelity.

Multiphasic Coacervates Assembled by Hydrogen Bonding and Hydrophobic Interactions.

Coacervation has emerged as a prevalent mechanism to compartmentalize biomolecules in living cells. Synthetic coacervates help in understanding the assembly process and mimic the functions of biological coacervates as simplified artificial systems. Though the molecular mechanism and mesoscopic properties of coacervates formed from charged coacervates have been well investigated, the details of the assembly and stabilization of nonionic coacervates remain largely unknown. Here, we describe a library of coacervate-forming polyesteramides and show that the water-tertiary amide bridging hydrogen bonds and hydrophobic interactions stabilize these nonionic, single-component coacervates. Analogous to intracellular biological coacervates, these coacervates exhibit "liquid-like" features with low viscosity and low interfacial energy, and form coacervates with as few as five repeating units. By controlling the temperature and engineering the molar ratio between hydrophobic interaction sites and bridging hydrogen bonding sites, we demonstrate the tuneability of the viscosity and interfacial tension of polyesteramide-based coacervates. Taking advantage of the differences in the mesoscopic properties of these nonionic coacervates, we engineered multiphasic coacervates with core-shell architectures similar to those of intracellular biological coacervates, such as nucleoli and stress granule-p-body complexes. The multiphasic structures produced from these synthetic nonionic polyesteramide coacervates may serve as a valuable tool for investigating physicochemical principles deployed by living cells to spatiotemporally control cargo partitioning, biochemical reaction rates, and interorganellar signal transport.

Influence of Core Type and Shell Thickness on Avian-Inspired Structural Colors Produced from Melanin Nanoparticle Assemblies.

Hollow melanosomes found in iridescent bird feathers, including violet-backed starlings and wild turkeys, enable the generation of diverse structural colors. It has been postulated that the high refractive index (RI) contrast between melanin (1.74) and air (1.0) results in brighter and more saturated colors. This has led to several studies that have synthesized hollow synthetic melanin nanoparticles and fabricated colloidal nanostructures to produce synthetic structural colors. However, these studies use hollow nanoparticles with thin shells (<20 nm), even though shell thicknesses as high as 100 nm have been observed in natural melanosomes. Here, we combine experimental and computational approaches to examine the influence of the varying polydopamine (PDA, synthetic melanin) shell thickness (0-100 nm) and core material on structural colors. Experimentally, a concomitant change in overall particle size and RI contrast makes it difficult to interpret the effect of a hollow or solid core on color. Thus, we utilize finite-difference time-domain (FDTD) simulations to uncover the effect of shell thickness and core on structural colors. Our FDTD results highlight that hollow particles with thin shells have substantially higher saturation than same-sized solid and core-shell particles. These results would benefit a wide range of applications including paints, coatings, and cosmetics.

Constraints on Knot Insertion, Not Internal Jamming, Control Polycatenane Translocation Dynamics through Crystalline Pores.

The translocation of polymers through pores and channels is an archetypal process in biology and is widely studied and exploited for applications in bio- and nanotechnology. In recent times, the translocation of polymers of various different topologies has been studied both experimentally and by computer simulation. However, in some cases, a clear understanding of the precise mechanisms that drive their translocation dynamics can be challenging to derive. Experimental methods are able to provide statistical details of polymer translocation, but computer simulations are uniquely placed to uncover a finer level of mechanistic understanding. In this work, we use high-throughput molecular simulations to reveal the importance that knot insertion rates play in controlling translocation dynamics in the small pore limit, where unexpected nonpower law behavior emerges. This work both provides new predictive understanding of polycatenane translocation and shows the importance of carefully considering the role of the definition of translocation itself.

Structure and Thermodynamics of Linear, Ring, and Catenane Polymers in Solutions and at Liquid-Liquid Interfaces.

In recent decades, advances in the syntheses of mechanically interlocked macromolecules, such as catenanes, have led to much greater interest in the applications of these complexes, from molecular motors and actuators to nanoscale computational memory and nanoswitches. Much remains to be understood, however, regarding how catenated ring compounds behave as a result of the effects of different solvents as well as the effects of solvent/solvent interfaces. In this work, we have investigated, using molecular dynamics simulations, the effects of solvation of poly(ethylene oxide) chains of different topologies─linear, ring, and [2]catenane─in two solvents both considered favorable toward PEO (water, toluene) and at the water/toluene interface. Compared to ring and [2]catenane molecules, the linear PEO chain showed the largest increase in size at the water/toluene interface compared to bulk water or bulk toluene. Perhaps surprisingly, observations indicate that the tendency of all three topologies to extend at the water/toluene interface may have more to do with screening the interaction between the two solvents than with optimizing specific solvent-polymer contacts.

Molecular Dynamics Simulation of Entangled Melts at High Rates: Identifying Entanglement Lockup Mechanism Leading to True Strain Hardening.

In the present work, molecular dynamics simulations are carried out based on the bead-spring model to indicate how the entanglement lockup manifests in the late stage of fast Rouse-Weissnberg number (WiR >>1) uniaxial melt stretching of entangled polymer melts. At high strains, distinct features show up to reveal the emergence of an increasingly tightened entanglement network. Chain tension can build up, peaking at the middle of the chain, to a level for chain scission, through accumulated interchain interactions, as if there is a tug-of-war ongoing for each load-bearing chain. Thanks to the interchain uncrossability, network junctions form by the pairing of two or more hairpins. It is hypothesized that the interchain entanglement at junctions can lockup through prevailing twist-like interchain couplings as long as WiR > 9. In this limit, a significant fraction of chains act like cyclic chains to form a network held by interchain uncrossability, and appreciable chain tension emerges.

Recent advancements in understanding the self-assembly of macroions in solution via molecular modeling.

Macroionic solutions behave quite differently from small ions in solution or colloids in suspension, representing a previously missing and very important transitional stage, and can further be connected to solutions of polyelectrolytes, including proteins and DNA (e.g., similarities between "blackberry" formation and virus capsid formation). While synthesis and characterization have produced an immense database regarding the self-assembly behavior of macroions in solution resulting in many empirical rules and guidelines, theory and simulations are sorely needed to connect these disparate threads into a cohesive and coherent narrative of macroionic solution theory and to provide guidance for future work. We recently developed a versatile coarse-grained model specifically designed for modelling the self-assembly of macroions in solution and have answered some of the most outstanding questions about the solution behavior of macroions including the source of the attractive force between like-charged macroions and how they self-assemble into a 2D monolayer structure.

Adsorptive Structure and Mobility on Carbon Nanotube Exteriors Using Benzoic Acid as a Molecular Probe of Amphiphilic Water Contaminants.

Benzoic acid is the simplest aromatic carboxylic acid that is also a common water contaminant. Its structural and amphiphilic properties are shared by many other contaminants of concern. Based on a molecular dynamics study, this work reports the competitive adsorption of benzoic acid with water on the curved exteriors of carbon nanotubes of varying oxygen content. With the help of cylindrically approximated pair correlation functions, carboxyl-carboxyl associations were found to serve as an additional mechanism providing stability to the adsorbed benzoic acid on tube exteriors. These associations are secondary to the main aromatic-aromatic interactions during the adsorption process and therefore were not sufficient to establish the energy hierarchy at the adsorbed state with increase in surface oxygen content. The same mechanism was previously ascribed to the adsorption of the structurally similar but bulkier tannic acid. Both water and benzoic acid were organized into numerous mobility groups and a correspondence was established between species residence time and the average translation time taken to escape the tube vicinity. Vigorous exchange of water molecules among the first adsorption shell, the second adsorption shell, and the immediate vicinity radially outside was estimated to take place within a short time of about 10 ps.

Toward the Rational Design of Organic Solar Photovoltaics: Application of Molecular Structure Methods to Donor Polymers.

Conjugated polymers are promising candidates in the design of polymer solar cell materials with suitable electronic properties. Recent studies show that the use of different functional groups as side chain in thiophene-based polymers changes the electronic and conformation structures. Here we design new thiophene-based molecules by replacing the hydrogen attached to the backbone of P3MT with electron-donating and electron-withdrawing groups. We then calculate the HOMO, LUMO, and HOMO-LUMO energy gap to quantify the theoretical merit of the new polymers as solar absorbers and their inter-ring torsional potential to understand their suitability to link together in high conductivity, extended conjugated systems. Calculations are done with first-principles density functional theory (DFT), implemented using B3LYP with dispersion function and 6-31G(d,p) as basis set. Our results show that the HOMO-LUMO gap is sensibly lowered by donating groups and we found that the substitution of the hydrogen with -NH2, and -F gives an energy gap lower than the energy gap of P3MT. The lowest energy gap was found when substituting with -NH2. Electron-withdrawing groups lower the HOMO, with the overall lowest found when -NO2 is used. -COCl, -CONH2, and -Cl give a steric hindrance greater than that of PTB7, which is set as reference. Our calculations show a possible approach to the rational design of donor materials when substituents are inserted systematically in a generic oligomer.

Rational Control of Self-Recognition of Macroionic γ-Cyclodextrin by Host-Guest Interaction with Super-Chaotropic Borate Cluster Ions.

We report a feasible method to control self-recognition during the self-assembly of a hydrophilic macroion, phosphate-functionalized γ-cyclodextrin (γ-CD-P), though host-guest interactions. We confirmed that γ-CD-P can form a host-guest complex with a super-chaotropic anion, namely the B12 F122- borate cluster, by using NMR spectroscopy and isothermal titration calorimetry. The loaded γ-CD-P, which has a higher charge density, can be distinguished from the uncomplexed γ-CD-P, leading to self-sorting behavior during the self-assembly process, confirmed by the formation of two types of individual supramolecular structures (Rh of ca. 57 nm and 18 nm, determined by light scattering) instead of hybrid structures in mixed dilute solution. This self-recognition behavior is accounted for by the difference in intermolecular electrostatic interactions arising from the loading.

Co-ion Effects in the Self-Assembly of Macroions: From Co-ions to Co-macroions and to the Unique Feature of Self-Recognition.

Macroions, as soluble ions with a size on the nanometer scale, show unique solution behavior different from those of simple ions and large colloidal suspensions. In macroionic solutions, the counterions are known to be important and well-explored. However, the role of co-ions (ions carrying the same type of charge as the macroions) is often ignored. Here, through experimental and simulation studies, we demonstrate the role of co-ions as a function of co-ion size on their interaction with the macroions (using {Mo72Fe30} and {SrPd12} as models) and the related self-assembly into blackberry-type structures in dilute solutions. Several regimes of unique co-ion effects are clearly identified: small ions (halides, oxoacid ions), subnanometer-scaled bulky ions (lacunary Keggin and dodecaborate ions), and those with sizes comparable to the macroions. Small co-ions have no observable effect on the self-assembly of fully hydrophilic {Mo72Fe30}, while due to hydrophobic interaction and intermolecular hydrogen bonds, the small co-ions show influences on the self-assembly of hydrophobic {SrPd12}. Subnanometer ions, a.k.a. "superchaotropic ions", are still too small to assemble into a blackberry by themselves, but they can coassemble with the macroions, showing a strong interaction with the macroionic system. When the co-ion size is comparable to that of the macroions, they assemble independently instead of assembling with the macroions, leading to the previously reported unique self-recognition phenomenon for macroions.

High Adsorption of Benzoic Acid on Single Walled Carbon Nanotube Bundles.

Removal of harmful chemicals from water is paramount to environmental cleanliness and safety. As such, need for materials that will serve this purpose is in the forefront of environmental research that pertains to water purification. Here we show that bundles of single walled carbon nanotubes (SWNTs), synthesized by direct thermal decomposition of ferrocene (Fe(C5H5)2), can remove emerging contaminants like benzoic acid from water with high efficiencies. Experimental adsorption isotherm studies indicate that the sorption capacity of benzoic acid on these carbon nanotubes (CNTs) can be as high as 375 mg/g, which is significantly higher (in some cases an order of magnitude) than those reported previously for other adsorbents of benzoic acid such as activated carbon cloth, modified bentonite and commercially available graphitized multiwall carbon nanotubes (MWNTs). Our Molecular Dynamics (MD) simulation studies of experimental scenarios provided major insights related to this process of adsorption. The MD simulations indicate that, high binding energy sites present in SWNT bundles are majorly responsible for their enhanced adsorptive behavior compared to isolated MWNTs. These findings indicate that SWNT materials can be developed as scalable materials for efficient removal of environmental contaminants as well as for other sorption-based applications.

Continuous Curvature Change into Controllable and Responsive Onion-like Vesicles by Rigid Sphere-Rod Amphiphiles.

We observe the formation of highly controllable and responsive onion-like vesicles by using rigid sphere-rod amphiphilic hybrid macromolecules, composed of charged, hydrophilic Keggin-type clusters (spheres) and hydrophobic rod-like oligofluorenes (OFs). Unlike the commonly used approach, which mainly relies on chain bending of flexible molecules to satisfy different curvatures in onion-like vesicles, the rigid hybrids form flexible interdigitations by tuning the angles between OFs, leading to the formation of bilayers with different sizes. The self-assembled vesicles possess complete onion-like structures from most inner to outer layers, and their size (layer number) can be accurately manipulated by different solution conditions including solvent polarity, ionic strength, temperature, and hybrid concentration, with fixed interbilayer distance under all conditions. Moreover, the vesicle size (layer number) shows excellent reversibility to the change of temperature. The charged feature of spheres, rod length, and overall hybrid architecture shows significant effects on the formation of such onion-like vesicles.

Probing calcium solvation by XAS, MD and DFT calculations.

The solvation shell structures of Ca2+ in aqueous and organic solutions probed by calcium L-edge soft X-ray absorption spectroscopy (XAS) and DFT/MD simulations show the coordination number of Ca2+ to be negatively correlated with the electrolyte concentration and the steric hindrance of the solvent molecule. In this work, the calcium L-edge soft XAS demonstrates its sensitivity to the surrounding chemical environment. Additionally, the total electron yield (TEY) mode is surface sensitive because the electron penetration depth is limited to a few nanometers. Thus this study shows its implications for future battery studies, especially for probing the electrolyte/electrode interface for electrochemical reactions under in situ/operando conditions.

Structure and Dynamics of Nanoconfined Water Between Surfactant Monolayers.

The properties of nanoconfined water arise in direct response to the properties of the interfaces that confine it. A great deal of research has focused on understanding how and why the physical properties of confined water differ greatly from the bulk. In this work, we have used all-atom molecular dynamics (MD) simulations to provide a detailed description of the structural and dynamical properties of nanoconfined water between two monolayers consisting of an archetypal ionic surfactant, cetrimonium bromide (CTAB, [CH3(CH2)15N(CH3)3]+Br-). Small differences in the area per surfactant of the monolayers impart a clear effect on the intrinsic density, mobility, and ordering of the interfacial water layer confined by the monolayers. We find that as the area per surfactant within a monolayer decreases, the mobility of the interfacial water molecules decreases in response. As the monolayer packing density decreases, we find that each individual CTAB molecule has a greater effect on the ordering of water molecules in its first hydration shell. In a denser monolayer, we observe that the effect of individual CTAB molecules on the ordering of water molecules is hindered by increased competition between headgroups. Therefore, when two monolayers with different areas per surfactant are used to confine a nanoscale water layer, we observe the emergence of noncentrosymmetry.

Adsorption of aromatic carboxylic acids on carbon nanotubes: impact of surface functionalization, molecular size and structure.

A large quantity of emerging contaminants are ionizable, and the ionized compounds display different adsorption behaviors than their neutral counterparts. In particular, a strong intermolecular force, negative charge assisted hydrogen bonding ((-)CAHB), was recently identified, which explains the unusually strong adsorption of negatively charged compounds on carbon nanotubes with oxygen-containing functional groups. However, most previous studies only probed molecules with one benzene ring. The adsorption of ionizable compounds with more than one benzene ring and additional functional groups has not been examined. This study investigated the effect of surface functionalization, molecular size and structure of six aromatic carboxylic acids on their adsorption on multi-walled carbon nanotubes (MWNTs) in batch reactors. In addition, the short-range interactions of the neutral acids with MWNTs were calculated to evaluate the effect of aromaticity and bulkiness. Hydrophobicity and electrostatic interactions dominate the intermolecular forces between ionized contaminants and MWNT surfaces. pH dependent octanol/water partitioning coefficient (Dow) is a more precise indicator of the adsorption of ionizable compounds on MWNTs. (-)CAHB is a significant force only for compounds with one benzene ring. Hydroxyl and carboxyl functional groups displayed similar capacity to form (-)CAHB, as indicated by the release of hydroxide ions.

Phase manipulation of topologically engineered AB-type multi-block copolymers.

Recent advances in the fundamental understanding of the ordered phases of multi-block copolymers (MBCPs) at the molecular level have attracted considerable scientific interest in recent years. Herein, by employing molecular dynamics simulation, we focus on the four typical systems: linear alternating, branch-like, star-like AB-type MBCPs and linear copolymers filled with nanoparticles (NPs). First, we establish the phase diagram for the linear tetrablock copolymers (ABAB) as a function of the composition ratio between A- and B-block, exhibiting six typical phase states. Furthermore, increasing the mutual repulsive interaction strength, the temperature and the periodic dynamic shearing cycle result in the merging of spheres, presenting a clear beginning of the order-to-order transition (OOT) behavior. Second, we examine the branch-like and star-like copolymers and find that increasing branch density significantly leads to the occurrence of phase transition. Particularly, we illustrate that the sphere configurations of the MBCPs can be described in terms of tail, loop and bridge conformations. Increasing the number of distinct blocks in linear alternating copolymers results in an enhancement of the bridge conformation, in which case some spheres are separated to smaller ones. Furthermore, for the tail conformation, we present a unified theoretical framework to rationalize the topological state of the chain arrangements of spheres and infer that the entanglements within the internal reaction layer between different A-blocks result in the inhomogeneous distribution of the spheres sizes even with controlled molecular weight and composition ratio between each block. Finally, we find that the ABAB tetrablock copolymers filled with moderate spherical NPs exhibit a clear OOT from spheres to double gyroid or cylinders. We infer that the maximum amount of the B-block within the second and/or third layers for the filled spherical NPs connects different NPs effectively, leading to the complicated OOT behavior. Generally, this fundamental study could provide some guidelines for designing and fabricating high performance BCPs by manipulating the formation of the ordered phases.