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In reticular chemistry, molecular building blocks are designed to create crystalline open frameworks. A key principle of reticular chemistry is that the most symmetrical networks are the likely outcomes of reactions, particularly when highly symmetrical building blocks are involved. The strategy of synthesizing low-dimensional networks aims to reduce explicitly the symmetry of the molecular building blocks. Here we report the spontaneous formation of hydrogen-bonded fibrous structures from trigonal prismatic building blocks, which were designed to form three-dimensional crystalline networks on account of their highly symmetrical structures. Utilizing different microscopic and spectroscopic techniques, we identify the structures at the early stages of the assembly process in order to and understand the growth mechanism. The symmetrical molecular building blocks are incorporated preferentially in the longitudinal direction, giving rise to anisotropic hydrogen-bonded porous organic nanotubes. Entropy-driven anisotropic growth provides micrometer-scale unidirectional nanotubes with high porosity. By combining experimental evidence and theoretical modeling, we have obtained a deep understanding of the nucleation and growth processes. Our findings offer fundamental insight into the molecular design of tubular structures. The nanotubes evolve further in the transverse directions to provide extended higher-order fibrous structures [nano- and microfibers], ultimately leading to large-scale interconnected hydrogen-bonded fiber-like structures with twists and turns. Our work provides fundamental understanding and paves the way for innovative molecular designs in low-dimensional networks.

Elicitation of effective antitumor immunity following cancer vaccination requires the selective activation of distinct effector cell populations and pathways. Here we report a therapeutic approach for generating potent T cell responses using a modular vaccination platform technology capable of inducing directed immune activation, termed the Protein-like Polymer (PLP). PLPs demonstrate increased proteolytic resistance, high uptake by antigen-presenting cells (APCs), and enhanced payload-specific T cell responses. Key design parameters, namely payload linkage chemistry, degree of polymerization, and side chain composition, were varied to optimize vaccine formulations. Linking antigens to the polymer backbone using an intracellularly cleaved disulfide bond copolymerized with a diluent amount of oligo(ethylene glycol) (OEG) resulted in the highest payload-specific potentiation of antigen immunogenicity, enhancing dendritic cell (DC) activation and antigen-specific T cell responses. Vaccination with PLPs carrying either gp100, E7, or adpgk peptides significantly increased the survival of mice inoculated with B16F10, TC-1, or MC38 tumors, respectively, without the need for adjuvants. B16F10-bearing mice immunized with gp100-carrying PLPs showed increased antitumor CD8+T cell immunity, suppressed tumor growth, and treatment synergy when paired with two distinct stimulator of interferon gene (STING) agonists. In a human papillomavirus-associated TC-1 model, combination therapy with PLP and 2′3′-cGAMP resulted in 40% of mice completely eliminating implanted tumors while also displaying curative protection from rechallenge, consistent with conferment of lasting immunological memory. Finally, PLPs can be stored long-term in a lyophilized state and are highly tunable, underscoring the unique properties of the platform for use as generalizable cancer vaccines.

An important goal of systems and synthetic biology is to produce high value chemical species in large quantities. Microcompartments, which are protein nanoshells encapsulating catalytic enzyme cargo, could potentially function as tunable nanobioreactors inside and outside cells to generate these high value species. Modifying the morphology of microcompartments through genetic engineering of shell proteins is one viable strategy to tune cofactor and metabolite access to encapsulated enzymes. However, this is a difficult task without understanding how changing interactions between the many different types of shell proteins and enzymes affect microcompartment assembly and shape. Here, we use multiscale molecular dynamics and experimental data to describe assembly pathways available to microcompartments composed of multiple types of shell proteins with varied interactions. As the average interaction between the enzyme cargo and the multiple types of shell proteins is weakened, the shell assembly pathway transitions from (i) nucleating on the enzyme cargo to (ii) nucleating in the bulk and then binding the cargo as it grows to (iii) an empty shell. Atomistic simulations and experiments using the 1,2-propanediol utilization microcompartment system demonstrate that shell protein interactions are highly varied and consistent with our multicomponent, coarse-grained model. Furthermore, our results suggest that intrinsic bending angles control the size of these microcompartments. Overall, our simulations and experiments provide guidance to control microcomparmtent size and assembly by modulating the interactions between shell proteins.

We investigate the usage of polyelectrolyte complex materials for water remediation purposes, specifically their ability to remove nanoplastics from water, on which there is currently little to no prior research. We demonstrate that oppositely charged random copolymers are effective at quantitatively removing nanoplastic contamination from aqueous solution. The mechanisms underlying this remediation ability are explored through computational simulations, with corroborating quartz crystal microbalance adsorption experiments. We find that hydrophobic nanostructures and interactions likely play an important role.

Size-asymmetric binary charged colloidal solutions can assemble into ionic colloidal crystals. These are often stabilized by ionic-type bonding, where the components with smaller size and charge sit at fixed points within the lattice of large particles. Here, we study the transition termed ionic to metallic bonding transition, by which the lattice of the smaller component melts while the crystal of the large particles is preserved, as in metallic bonding. We simulate a charged colloidal crystal in equilibrium with a solution containing small colloidal particles and counterions using the Coulomb interaction between the finite-size components. We find ionic to metallic first-order transitions by increasing either the temperature or the concentration of the small particles in the solution. The transition is accompanied by a lattice expansion and increased absorption of small particles into the crystal. We compute the free energies of the ionic and metallic states using the Madelung constant and Wigner–Seitz cell approaches, respectively, combined with the quasi-harmonic lattice model. The calculation reproduces the simulated transition and reveals that the enthalpic gain is more pronounced than the entropic gain in the transition from ionic to metallic bonding when material is exchanged with the solution.

Effective control over the thermal behavior and mechanical strength of polymeric materials has been highly sought for decades and continues to this day, particularly with the urgent demand for highly durable energy storage devices and soft electronics, to name a few. Here, we report a simple yet versatile approach to fine-tune the glass transition range of a family of ionomers via their side-chain structure and charge fraction. We analyze ionomers of poly(3-sulfopropyl methacrylate-ran-methyl methacrylate) that are synthesized by conventional free-radical polymerization. Using derivative heat flow curves from differential scanning calorimetry, we find that above a critical low charge-carrying side-chain fraction (fq), the glass transition temperature shifts to higher values and the glass transition breadth increases significantly in response to thermal treatment. After several thermal cycles, values of glass transition breadth as high as 90–104 °C were obtained, and the evolution from one glass transition regime to two distinct, contiguous glass transition regimes was evident. Quenched molecular dynamics simulations elucidate the roles of several key design parameters of the ionomers near the glass transition, specifically the importance of the charge-carrying polymer side chains. Analysis of energetics and structural relaxation dynamics reveals the effects of strong ionic correlations in a low dielectric constant medium and the side-chain mobility on the transition from liquid to supercooled liquid. As fqincreases beyond a critical value and is accompanied by thermal treatment, the local ionic concentrations are more heterogeneous, and the distribution of the ionic cluster sizes becomes broader at the transition point. The resulting enhanced degree of compositional and dynamic heterogeneity leads to a shift in the supercooled liquid transition toward higher temperatures.

The use of surfactants to attract dissolved ions to water surfaces and interfaces is an essential step in both solvent-based and solvent-free separation processes. We have studied the interactions of lanthanide ions in the aqueous subphase with monolayers of dihexadecyl phosphate at air–water interfaces. With heavier lanthanides (atomic number Z≥ 65) in the subphase, the floating layer can be compressed to an area/molecule of about half the molecular cross section, indicating bilayer formation. X-ray fluorescence and reflectivity data support this conclusion. In the presence of lighter lanthanides (Z< 65), only monolayers are observed. Subphase-concentration-dependent studies using Er3+(heavier) and Nd3+(lighter) lanthanides show a stepwise progression, with ions attaching to the monolayer only when the solution concentration is >3 × 10–7M. Above ∼10–5M, bilayers form but only in the presence of the heavier lanthanide. Grazing incidence X-ray diffraction shows evidence of lateral ion–ion correlations in the bilayer structure but not in monolayers. Explicit solvent all-atom molecular dynamics simulations confirm the elevated ion–ion correlation in the bilayer system. This bilayer structure isolates heavier lanthanides but not lighter lanthanides from an aqueous solution and is therefore a potential mechanism for the selective separation of heavier lanthanides.

Protein enzymes have shown great potential in numerous technological applications. However, the design of supporting materials is needed to preserve protein functionality outside their native environment. Direct enzyme–polymer self-assembly offers a promising alternative to immobilize proteins in an aqueous solution, achieving higher control of their stability and enzymatic activity in industrial applications. Herein, we propose a modeling-based design to engineering hydrogels of cytochrome P450 and of PETase with styrene/2-vinylpyridine (2VP) random copolymers. By tuning the copolymer fraction of polar groups and of charged groups via quaternization of 2VP for coassembly with cytochrome P450 and via sulfonation of styrene for coassembly with PETase, we provide quantitative guidelines to select either a protein–polymer hydrogel structure or a single-protein encapsulation. The results highlight that, regardless of the protein surface domains, the presence of polar interactions and hydration effects promote the formation of a more elongated enzyme–polymer complex, suggesting a membrane-like coassembly. On the other hand, the effectiveness of a single-protein encapsulation is reached by decreasing the fraction of polar groups and by increasing the charge fraction up to 15%. Our computational analysis demonstrates that the enzyme–polymer assemblies are first promoted by the hydrophobic interactions which lead the protein nonpolar residues to achieve the maximum coverage and to play the role of the most robust contact points. The mechanisms of coassembly are unveiled in the light of both protein and polymer physical-chemistry, providing bioconjugate phase diagrams for the optimal material design.

Self-organized shells are fundamental in biological compartmentalization. They protect genomic material or enclose enzymes to aid the metabolic process. Studies of crystalline shells have shown the importance of the mechanical properties of building units in the shell morphology. However, the mechanism underlying the morphology of multicomponent assemblies is still poorly understood. Here, we analyze multicomponent closed shells that have different mechanical properties. By minimizing elastic energy, we show that heterogeneous bending rigidities regulate the surface pattern into circular, spikes, and ridge shapes. Interestingly, our continuum elasticity model recovers the patterns that have been proposed in bacterial microcompartments (BMCs), which are self-organized protein shells that aid the breakdown of complex molecules and allow bacteria to survive in hostile environments. In addition, our work elucidates the principles of pattern formation that can be used to design and engineer multicomponent microcompartments with a specific surface distribution of the components.

Bacterial microcompartments compartmentalize the enzymes that aid chemical and energy production in many bacterial species. They are postulated to help bacteria survive in hostile environments. Metabolic engineers are interested in repurposing these organelles for non-native functions. Here, we use computational, theoretical, and experimental approaches to determine mechanisms that effectively control microcompartment self-assembly. We find, via multiscale modeling and mutagenesis studies, the interactions responsible for the binding of hexamer-forming proteins in a model system, the propanediol utilization bacterial microcompartments from Salmonella entericaserovar Typhimurium LT2. We determine how the changes in the microcompartment hexamer protein preferred angles and interaction strengths can modify the assembled morphologies. We demonstrate that such altered strengths and angles are achieved via amino acid mutations. A thermodynamic model provides guidelines to design microcompartments of various morphologies. These findings yield insight in controlled protein assembly and provide principles for assembling microcompartments for biochemical or energy applications as nanoreactors.

Colloidal particles are ubiquitous in biology and in everyday products such as milk, cosmetics, lubricants, paints, or drugs. The stability and aggregation of colloidal suspensions are of paramount importance in nature and in diverse nanotechnological applications, including the fabrication of photonic materials and scaffolds for biological assemblies, gene therapy, diagnostics, targeted drug delivery, and molecular labeling. Electrolyte solutions have been extensively used to stabilize and direct the assembly of colloidal particles. In electrolytes, the effective electrostatic interactions among the suspended colloids can be changed over various length scales by tuning the ionic concentration. However, a major limitation is gelation or flocculation at high salt concentrations. This is explained by classical theories, which show that the electrostatic repulsion among charged colloids is significantly reduced at high electrolyte concentrations. As a result, these screened colloidal particles are expected to aggregate due to short-range attractive interactions or dispersion forces as the salt concentration increases. We discuss here a robust, tunable mechanism for colloidal stability by which large counterions prevent highly charged nanoparticles from aggregating in salt solutions with concentrations up to 1 M. Large counterions are shown to generate a thicker ionic cloud in the proximity of each charged colloid, which strengthens short-range repulsions among colloidal particles and also increases the corresponding renormalized colloidal charge perceived at larger separation distances. These effects thus provide a reliable stabilization mechanism in a broad range of biological and synthetic colloidal suspensions.

Crystalline vesicles are promising nanomaterials due to their mechanical stability in various environments. To control their fabrication, it is essential to understand the effects of different experimental conditions on crystallization. Here we perform atomistic molecular dynamics simulations of anionic lipid membranes of 1,2-dilauroyl-sn-glycero-3-phosphol-l-serine. In the presence of Na+monovalent counterions, we access the phase transition from the liquid-like disordered liquid-crystalline phase to the ordered gel phase by lowering the temperature of the system. The phase transition is conclusivelyevidenced by the scattering structure factor. Quantitativecalculations show that the enhancement of the intertail van der Waals interaction (about −6 kBT) plays a dominant role in driving the phase transition rather than the increase in the cohesive interaction (−0.5 kBT) between lipids and counterions. Meanwhile, in the presence of multivalent counterions of Zn2+or La3+the gel phase is found throughout the temperature range investigated. Moreover, the van der Waals interaction per hydrocarbon group is ∼20% stronger in the gel phase (∼ −1.8 kBTregardless of the counterions) than in the liquid-crystalline phase (−1.5 kBT).

Epitaxial growth of DNA-functionalized nanoparticles is used to grow extended superlattices with a preferred orientation for optimizing the physical properties of metamaterials for real applications. Like any solid in nature, superlattices can contain different kinds of structural defects, which significantly alter their physical properties. Further development of these materials requires a deeper understanding of, as well as precise control over, structural defect formation. Here we use Monte Carlo simulations to conduct a systematic study of the equilibrium structures of the adsorbed nanoparticle monolayers by changing the binding energies of different attachment sites. The simulations show two main results. First, the structural defects form one-dimensional clusters with an exponential length distribution. Second, these linear defects exhibit spontaneous symmetry breaking and undergo a liquid crystal phase transition. Subsequently, a mean-field approach is introduced to provide theoretical descriptions for the system. Our theory matches with the simulation results. We anticipate that this theoretical framework will be highly applicable to other two-dimensional assemblies. Our work demonstrates that defects can be engineered to design two-dimensional superlattices with interesting physical properties.

The encapsulation of enzymes within porous materials has shown great promise, not only in protecting the enzymes from denaturation under nonbiological environments, but also, in some cases, in facilitating their enzymatic reaction rates at favorable reaction conditions. While a number of hypotheses have been developed to explain this phenomenon, the detailed structural changes of the enzymes upon encapsulation within the porous material, which are closely related to their activity, remain largely elusive. Herein, the structural change of cytochrome c (Cyt c) upon encapsulation within a hierarchical metal–organic framework, NU-1000, is investigated through a combination of experimental and computational methods, such as electron paramagnetic resonance, solid-state ultraviolet–visible spectroscopy, and all-atom explicit solvent molecular dynamics simulations. The enhanced catalytic performance of Cyt c after being encapsulated within NU-1000 is supported by the physical and in silico observations of a change around the heme ferric active center.

The surface of proteins is vital in determining protein functions. Herein, a program, Protein Surface Printer (PSP), is built that performs multiple functions in quantifying protein surface domains. Two proteins, PETase and cytochrome P450, are used to validate that the program supports atomistic simulations with different combinations of programs and force fields. A case study is conducted on the structural analysis of the spike proteins of SARS-CoV-2 and SARS-CoV and the human cell receptor ACE2. Although the surface domains of both spike proteins are highly similar, their receptor-binding domains (RBDs) and the O-linked glycan domains are structurally different. The O-linked glycan domain of SARS-CoV-2 is highly positively charged, which may promote binding to negatively charged human cells.

The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein plays a crucial role in binding the human cell receptor ACE2 that is required for viral entry. Many studies have been conducted to target the structures of RBD–ACE2 binding and to design RBD-targeting vaccines and drugs. Nevertheless, mutations distal from the SARS-CoV-2 RBD also impact its transmissibility and antibody can target non-RBD regions, suggesting the incomplete role of the RBD region in the spike protein–ACE2 binding. Here, in order to elucidate distant binding mechanisms, we analyze complexes of ACE2 with the wild-type spike protein and with key mutants vialarge-scale all-atom explicit solvent molecular dynamics simulations. We find that though distributed approximately 10 nm away from the RBD, the SARS-CoV-2 polybasic cleavage sites enhance, viaelectrostatic interactions and hydration, the RBD–ACE2 binding affinity. A negatively charged tetrapeptide (GluGluLeuGlu) is then designed to neutralize the positively charged arginine on the polybasic cleavage sites. We find that the tetrapeptide GluGluLeuGlu binds to one of the three polybasic cleavage sites of the SARS-CoV-2 spike protein lessening by 34% the RBD–ACE2 binding strength. This significant binding energy reduction demonstrates the feasibility to neutralize RBD–ACE2 binding by targeting this specific polybasic cleavage site. Our work enhances understanding of the binding mechanism of SARS-CoV-2 to ACE2, which may aid the design of therapeutics for COVID-19 infection.

Understanding viral assembly pathways is of critical importance to biology, medicine, and nanotechology. Here, we study the assembly path of a system with various structures, the simian vacuolating virus 40 (SV40) polymorphs. We simulate the templated assembly process of VP1 pentamers, which are the constituents of SV40, into icosahedal shells made of N= 12 pentamers (T= 1). The simulations include connections formed between pentamers by C-terminal flexible lateral units, termed here “C-terminal ligands”, which are shown to control assembly behavior and shell dynamics. The model also incorporates electrostatic attractions between the N-terminal peptide strands (ligands) and the negatively charged cargo, allowing for agreement with experiments of RNA templated assembly at various pH and ionic conditions. During viral assembly, pentamers bound to any template increase its effective size due to the length and flexibility of the C-terminal ligands, which can connect to other VP1 pentamers and recruit them to a partially completed capsid. All closed shells formed other than the T= 1 feature the ability to dynamically rearrange and are thus termed “pseudo-closed”. The N= 13 shell can even spontaneously “self-correct” by losing a pentamer and become a T= 1 capsid when the template size fluctuates. Bound pentamers recruiting additional pentamers to dynamically rearranging capsids allow closed shells to continue growing viathe pseudo-closed growth mechanism, for which experimental evidence already exists. Overall, we show that the C-terminal ligands control the dynamic assembly paths of SV40 polymorphs.

Complexation of oppositely charged macromolecules is essential in several biological phenomena. Recent reports have demonstrated the importance of DNA local flexibility in governing liquid–liquid phase separation (LLPS), a ubiquitous phenomenon thought to drive membraneless cellular organization. Inspired by this, we perform coarse-grained molecular dynamics simulations to study the role of chain flexibility in the complexation of short negatively charged polyelectrolytes with long positively charged polyelectrolytes. At low ionic strengths, spontaneous segregation of chains into a condensed (polymer-rich) phase and a supernatant (polymer-depleted) phase is observed. When both the polyanion and polycation are flexible (flexible–flexible complex), denser complexes with a higher degree of structural correlation form, with fewer free chains released into the supernatant, compared to the case when the polyanion is rigid (rigid–flexible complex), in agreement with the LLPS experiments. Free chains are in rapid exchange between the supernatant and the condensed phase. The partitioning of salt ions in the two phases depends on chain flexibility, with salt ions partitioned more into the condensed phase for flexible–flexible complexes. Interestingly, at intermediate to high salt concentrations, flexible–flexible complexes form multiple equilibrium finite-size clusters, suggesting nanophase to microphase segregated structures, while rigid–flexible complexes tend to condense into a single complex. The results provide molecular-level insights into LLPS of asymmetric polyelectrolyte complexation and give guidelines for assembling oppositely charged macromolecules with different degrees of molecular flexibility.

Solid polymer electrolytes are considered a promising alternative to traditional liquid electrolytes in energy storage applications because of their good mechanical properties, and excellent thermal and chemical stability. A gap, however, still exists in understanding ion transport mechanisms and improving ion transport in solid polymer electrolytes. Therefore, it is crucial to bridge composition–structure and structure–property relationships. Here, we demonstrate that size asymmetry, λ, represented by the ratio of counterion to charged monomer size, plays a key role both in the nanostructure and in the ionic dynamics. More specifically, when the nanostructure is modified by an external electric field such that the mobility cannot be described by linear response theory, two situations arise. The ionic mobility increases as λ decreases (small counterions) in the weak electrostatics (high dielectric constant) regime, whereas in systems with strong electrostatic interactions, ionomers with higher size symmetry (λ ≈ 1) display higher ionic mobility. Moreover, ion transport is found to be dominated by the hopping of the ions and not by moving ionic clusters (also known as “vehicular” charge transport). These results serve as a guide for designing ion-containing polymers for ion transport related applications.

Label-free in situX-ray scattering from protein spherical nucleic acids (Pro-SNAs, consisting of protein cores densely functionalized with covalently bound DNA) was used to elucidate the enzymatic reaction pathway for the DNase I-induced degradation of DNA. Time-course small-angle X-ray scattering (SAXS) and gel electrophoresis reveal a two-state system with time-dependent populations of intact and fully degraded DNA in the Pro-SNAs. SAXS shows that in the fully degraded state, the DNA strands forming the outer shell of the Pro-SNA were completely digested. SAXS analysis of reactions with different Pro-SNA concentrations reveals a reaction pathway characterized by a slow, rate determining DNase I-Pro-SNA association, followed by rapid DNA hydrolysis. Molecular dynamics (MD) simulations provide the distributions of monovalent and divalent ions around the Pro-SNA, relevant to the activity of DNase I. Taken together, in situSAXS in conjunction with MD simulations yield key mechanistic and structural insights into the interaction of DNA with DNase I. The approach presented here should prove invaluable in probing other enzyme-catalyzed reactions on the nanoscale.

Light-sensitive particles have been shown to stratify in solution in a way that changes the colour of the whole suspension. The system forms a colour-changing ink that could make electronic paper a viable technology.

We demonstrate that a highly charged polyelectrolyte confined in a spherical cavity undergoes reversible transformations between amorphous conformations and a four-fold symmetry morphology as a function of dielectric mismatch between the media inside and outside the cavity. Surface polarization due to dielectric mismatch exhibits an extra “confinement” effect, which is most pronounced within a certain range of the cavity radius and the electrostatic strength between the monomers and counterions and multivalent counterions. For cavities with a charged surface, surface polarization leads to an increased amount of counterions adsorbed in the outer side, further compressing the confined polyelectrolyte into a four-fold symmetry morphology. The equilibrium conformation of the chain is dependent upon several key factors including the relative permittivities of the media inside and outside the cavity, multivalent counterion concentration, cavity radius relative to the chain length, and interface charge density. Our findings offer insights into the effects of dielectric mismatch in packaging and delivery of polyelectrolytes across media with different relative permittivities. Moreover, the reversible transformation of the polyelectrolyte conformations in response to environmental permittivity allows for potential applications in biosensing and medical monitoring.

Rebinding kinetics of molecular ligands plays a key role in the operation of biomachinery, from regulatory networks to protein transcription, and is also a key factor in design of drugs and high-precision biosensors. In this study, we investigate initial release and rebinding of ligands to their binding sites grafted on a planar surface, a situation commonly observed in single-molecule experiments and that occurs in vivo, e.g., during exocytosis. Via scaling arguments and molecular dynamic simulations, we analyze the dependence of nonequilibrium rebinding kinetics on two intrinsic length scales: the average separation distance between the binding sites and the total diffusible volume (i.e., height of the experimental reservoir in which diffusion takes place or average distance between receptor-bearing surfaces). We obtain time-dependent scaling laws for on rates and for the cumulative number of rebinding events. For diffusion-limited binding, the (rebinding) on rate decreases with time via multiple power-law regimes before the terminal steady-state (constant on-rate) regime. At intermediate times, when particle density has not yet become uniform throughout the diffusible volume, the cumulative number of rebindings exhibits a novel, to our knowledge, plateau behavior because of the three-dimensional escape process of ligands from binding sites. The duration of the plateau regime depends on the average separation distance between binding sites. After the three-dimensional diffusive escape process, a one-dimensional diffusive regime describes on rates. In the reaction-limited scenario, ligands with higher affinity to their binding sites (e.g., longer residence times) delay entry to the power-law regimes. Our results will be useful for extracting hidden timescales in experiments such as kinetic rate measurements for ligand-receptor interactions in microchannels, as well as for cell signaling via diffusing molecules.

Protein aggregation has been observed inside cells and holds true for membraneless organelles. The precise understanding of protein dimerization is a prerequisite for manipulating protein aggregation, which is promising for elevating enzyme concentration to enhance their catalytic performance. Here, the dimerization of two industrially important enzymes of cytochrome P450 (P450) and organophosphorus hydrolase (OPH) is investigated using all-atom explicit solvent molecular dynamics simulations, umbrella sampling, and protein–protein docking calculations. The calculated potentials of mean force of dimer–monomer dissociation demonstrate that the dimeric forms are more stable with the free energy barrier of around 60 kJ/mol for P450 and 101 kJ/mol for OPH. The docking calculations on the OPH dimer evidence the uniqueness of the native orientation. The protein dimers form “mirror”-like orientations with some degree of rotation. Such signature orientations are interpreted based on the predominant polar amino acids in the contact regime. In the dimer conformations, the active sites are exposed. This work highlights the crucial roles of the polar and nonpolar protein surface domains to form enzymatically active protein dimer aggregates. Our work will potentially aid the design of molecules that can deliver and protect native protein function in various environments.

Quantitatively understanding the self-assembly of amphiphilic macromolecules at liquid–liquid interfaces is a fundamental scientific concern due to its relevance to a broad range of applications including bottom-up nanopatterning, protein encapsulation, oil recovery, drug delivery, and other technologies. Elucidating the mechanisms that drive assembly of amphiphilic macromolecules at liquid–liquid interfaces is challenging due to the combination of hydrophobic, hydrophilic, and Coulomb interactions, which require consideration of the dielectric mismatch, solvation effects, ionic correlations, and entropic factors. Here we investigate the self-assembly of a model block copolymer with various charge fractions at the chloroform–water interface. We analyze the adsorption and conformation of poly(styrene)-block-poly(2-vinylpyridine) (PS-b-P2VP) and of the homopolymer poly(2-vinylpyridine) (P2VP) with varying charge fraction, which is controlled via a quaternization reaction and distributed randomly along the backbone. Interfacial tension measurements show that the polymer adsorption increases only marginally at low charge fractions (<5%) but increases more significantly at higher charge fractions for the copolymer, while the corresponding randomly charged P2VP homopolymer analogues display much more sensitivity to the presence of charged groups. Molecular dynamics (MD) simulations of the experimental systems reveal that the diblock copolymer (PS-b-P2VP) interfacial activity could be mediated by the formation of a rich set of complex interfacial copolymer aggregates. Circular domains to elongated stripes are observed in the simulations at the water–chloroform interface as the charge fraction increases. These structures are shown to resemble the spherical and cylindrical helicoid structures observed in bulk chloroform as the charge fraction increases. The self-assembly of charge-containing copolymers is found to be driven by the association of the charged component in the hydrophilic block, with the hydrophobic segments extending away from the hydrophilic cores into the chloroform phase.

We examine the effects of ionic correlations and dielectric mismatch on the miscibility of ionomer blends with a hybrid ionomer blend thermodynamic liquid state theory approach. The ionomer (A) has a dielectric constant ϵAand low charge fraction (<10%). First, explicit ions coarse-grained molecular dynamics simulations with no dielectric mismatch verify that ionic correlations lead to segregation, in agreement with the theory, which includes nonlinear and many-body effects. Then, the extended theory that incorporates dielectric mismatch shows that strong ionic correlations dominate the phase behavior when the dielectric mismatch is low. However, solvation effects dominate when the mismatch is high (ϵA≫ ϵB), where the preference of the ions to be solvated in a higher dielectric medium is balanced by the entropic driving force for a uniform dielectric constant throughout the system. When salt is added as a third component, dielectric mismatch is significant only at low salt concentrations.

We report on a theoretical study of the phase behavior of polymer blends with hydrogen-bonding (HB) groups using the mean-field approximation. The hydrogen bonds are modeled as saturable bonds. We find the parametric conditions for lower and upper critical solution temperatures (LCST and UCST) and the eutectic behavior for the HB polymer blends. We quantify the conditions for the miscibility, partial miscibility, and immiscibility of HB polymer blends. We evaluate the conditions for the applicability of the Flory–Huggins theory to HB polymers by analyzing the composition dependence of the effective Flory–Huggins interaction parameter χeff. We use the polymer self-consistent field theory together with our model to compute the interfacial tension between coexisting phases in HB blends and find that intercomponent hydrogen bonding may significantly reduce the interfacial tension relative to a regular polymer blend at the same degree of segregation.

Protein–spherical nucleic acid conjugates (Pro-SNAs) are an emerging class of bioconjugates that have properties defined by their protein cores and dense shell of oligonucleotides. They have been used as building blocks in DNA-driven crystal engineering strategies and show promise as agents that can cross cell membranes and affect both protein and DNA-mediated processes inside cells. However, ionic environments surrounding proteins can influence their activity and conformational stability, and functionalizing proteins with DNA substantively changes the surrounding ionic environment in a nonuniform manner. Techniques typically used to determine protein structure fail to capture such irregular ionic distributions. Here, we determine the counterion radial distribution profile surrounding Pro-SNAs dispersed in RbCl with 1 nm resolution through in situanomalous small-angle X-ray scattering (ASAXS) and classical density functional theory (DFT). SAXS analysis also reveals the radial extension of the DNA and the linker used to covalently attach the DNA to the protein surface. At the experimental salt concentration of 50 mM RbCl, Rb+cations compensate ∼90% of the negative charge due to the DNA and linker. Above 75 mM, DFT calculations predict overcompensation of the DNA charge by Rb+. This study suggests a method for exploring Pro-SNA structure and function in different environments through predictions of ionic cloud densities as a function of salt concentration, DNA grafting density, and length. Overall, our study demonstrates that solution X-ray scattering combined with DFT can discern counterionic distribution and submolecular features of highly charged, complex nanoparticle constructs such as Pro-SNAs and related nucleic acid conjugate materials.

Understanding the electrostatic interactions in ion-containing polymers is crucial to better design shape memory polymers and ion-conducting membranes for multiple energy storage and conversion applications. In molten polymers, the dielectric permittivity is low, generating strong ionic correlations that lead to clustering of the charges. Here, we investigate the influence of electrostatic interactions on the nanostructure of randomly charged polymers (ionomers) using coarse-grained molecular dynamics simulations. Densely packed branched structures rich in charged species are found as the strength of the electrostatic interactions increases. Polydispersity in charge fraction and composition combined with ion correlations leads to percolated nanostructures with long-range fluctuations. We identify the percolation point at which the ionic branched nanostructures percolate and offer a rigorous investigation of the statistics of the shape of the aggregates. The extra degree of freedom introduced by the charge polydispersity leads to bicontinuous structures with a broad range of compositions, similar to neutral A–B random copolymers, as well as to desirable percolated ionic structure in randomly charged-neutral diblock copolymers. These findings provide insight into the design of conducting and robust nanostructures in ion-containing polymers.

The propulsion of micro- and nanoparticles using ultrasound is an attractive strategy for the remote manipulation of colloidal matter using biocompatible energy inputs. However, the physical mechanisms underlying acoustic propulsion are poorly understood, and our ability to transduce acoustic energy into different types of particle motions remains limited. Here, we show that the three-dimensional shape of a colloidal particle can be rationally engineered to direct desired particle motions powered by ultrasound. We investigate the dynamics of gold microplates with twisted star shape (Cnhsymmetry) moving within the nodal plane of a uniform acoustic field at megahertz frequencies. By systematically perturbing the parametric shape of these “spinners”, we quantify the relationship between the particle shape and its rotational motion. The experimental observations are reproduced and explained by hydrodynamic simulations that describe the steady streaming flows and particle motions induced by ultrasonic actuation. Our results suggest how particle shape can be used to design colloids capable of increasingly complex motions powered by ultrasound.

Directed crystallization of a large variety of nanoparticles, including proteins, via DNA hybridization kinetics has led to unique materials with a broad range of crystal symmetries. The nanoparticles are functionalized with DNA chains that link neighboring functionalized units. The shape of the nanoparticle, the DNA length, the sequence of the hybridizing DNA linker, and the grafting density determine the crystal symmetries and lattice spacing. By carefully selecting these parameters, one can, in principle, achieve all the symmetries found for both atomic and colloidal crystals of asymmetric shapes as well as new symmetries and can drive transitions between them. A scale-accurate coarse-grained model with explicit DNA chains provides the design parameters, including the degree of hybridization, to achieve specific crystal structures. The model also provides surface energy values to determine the shape of defect-free single crystals with macroscopic anisotropic properties, which has potential for the fabrication of materials with specific optical and mechanical properties.

Vitrimers are associative covalent adaptable networks that undergo reversible bond-exchange reactions while maintaining a fixed cross-linking density with changing temperature. To date, experimental studies that rely on macroscopic rheology have not been able to reveal topological changes and microscopic dynamics in these materials. Here, coarse-grained molecular dynamics simulations combined with a Monte Carlo method are implemented to investigate the topological structural changes, microscopic dynamics, and linear rheology of unentangled side-chain-linked vitrimers in conjunction with the sticky Rouse model (SRM). We find that there is a minor variation in the topological structure with temperature. The dynamic heterogeneities of the bond-exchange behavior and the system dynamics increase remarkably when approaching the topological freezing transition temperature Tv. Quantitative agreement between the simulation results and the SRM predictions is observed for the stress relaxation, elastic and loss moduli, and the relative mean-squared displacement, especially at the intermediate- and long-time or low-frequency regimes, where the time–temperature superposition principle is satisfied. We obtain a scaling collapse curve for the dynamic bond relaxation time, the zero-shear viscosity, and the horizontal shift factors without introducing any parameters, suggesting that the microscopic and macroscopic dynamics exhibit a similar relaxation behavior even in the presence of loop defects. Moreover, these results are in good agreement with those predicted by the SRM, indicating that the linear rheology of unentangled vitrimers with a fast bond-exchange rate can be analyzed via a single-chain approach based on the SRM.

Patchy colloids are attractive as programmable building blocks for metamaterials. Inverse patchy colloids, in which a charged surface is decorated with patches of the opposite charge, are additionally noteworthy as models for heterogeneously charged biological materials such as proteins. We study the phases and aggregation behavior of a single charged patch in an oppositely charged colloid with a single-site model. This single-patch inverse patchy colloid model shows a large number of phases when varying patch size. For large patch sizes we find ferroelectric crystals, while small patch sizes produce cross-linked gels. Intermediate values produce monodisperse clusters and unusual worm structures that preserve finite ratios of area to volume. The polarization observed at large patch sizes is robust under extreme disorder in patch size and shape. We examine phase-temperature dependence and coexistence curves and find that large patch sizes produce polarized liquids, in contrast to mean-field predictions. Finally, we introduce small numbers of unpatched charged colloids. These can either suppress or encourage aggregation depending on their concentration and the size of the patches on the patched colloids. These effects can be exploited to control aggregation and to measure effective patch size.

Solutions at high salt concentrations are used to crystallize or segregate charged colloids, including proteins and polyelectrolytes via a complex mechanism referred to as “salting-out”. Here, we combine small-angle X-ray scattering (SAXS), molecular dynamics (MD) simulations, and liquid-state theory to show that salting-out is a long-range interaction, which is controlled by electrolyte concentration and colloid charge density. As a model system, we analyze Au nanoparticles coated with noncomplementary DNA designed to prevent interparticle assembly via Watson–Crick hybridization. SAXS shows that these highly charged nanoparticles undergo “gas” to face-centered cubic (FCC) to “glass-like” transitions with increasing NaCl or CaCl2concentration. MD simulations reveal that the crystallization is concomitant with interparticle interactions changing from purely repulsive to a “long-range potential well” condition. Liquid-state theory explains this attraction as a sum of cohesive and depletion forces that originate from the interelectrolyte ion and electrolyte–ion–nanoparticle positional correlations. Our work provides fundamental insights into the effect of ionic correlationsin the salting-out mechanism and suggests new routes for the crystallization of colloids and proteins using concentrated salts.

The power conversion efficiency of organic solar cells (OSCs) could benefit from systematic studies to improve bulk heterojunction (BHJ) morphology by modifying donor compounds. Supramolecular self-assembly is an attractive strategy to combine the beneficial properties of polymeric donors, such as a well-controlled morphology, with the homogeneous composition of small molecule donors for OSCs. We report here on two tripodal “star-shaped” small-molecule donor compounds based on diketopyrrolopyrrole (DPP) side chains for solution-processed BHJ OSCs. The tripod molecules were found not to aggregate in solution or form crystalline domains in thin films when a branched alkyl chain (2-ethylhexyl) substituent was used, whereas linear (docedecyl) alkyl chains promote the formation of one-dimensional (1D) nanowires and more crystalline domains in the solid state. We demonstrate that the 1D self-assembly of these tripods enhances the performance of the corresponding solution-processed OSCs by 50%, which is attributed to the significant increase in the fill factor of devices resulting from a reduction of trap states.

Understanding and controlling vesicle shapes is a fundamental challenge in biophysics and materials design. In this paper, we design dynamic protocols for enlarging the shape space of both fluid and crystalline vesicles beyond the equilibrium zone. By removing water from within the vesicle at different rates, we numerically produced a series of dynamically trapped stable vesicle shapes for both fluid and crystalline vesicles in a highly controllable fashion. In crystalline vesicles that are continuously dehydrated, simulations show the initial appearance of small flat areas over the surface of the vesicles that ultimately merge to form fewer flat faces. In this way, the vesicles transform from a fullerene-like shape into various faceted polyhedrons. We perform analytical elasticity analysis to show that these salient features are attributable to the crystalline nature of the vesicle. The potential to use dynamic protocols, such as those used in this study, to engineer vesicle shape transformations is helpful for exploiting the richness of vesicle geometries for desired applications.

Charged colloids and proteins in aqueous solutions interact via short-range attractions and long-range repulsions (SALR) and exhibit complex structural phases. These include homogeneously dispersed monomers, percolated monomers, clusters, and percolated clusters. We report the structural architectures of simple charged systems in the form of spherical, Keggin-type heteropolyanions (HPAs) by small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. Structure factors obtained from the SAXS measurements show that the HPAs interact via SALR. Concentration and temperature dependences of the structure factors for HPAs with −3e(eis the charge of an electron) charge are consistent with a mixture of nonassociated monomers and associated randomly percolated monomers, whereas those for HPAs with −4eand −5echarges exhibit only nonassociated monomers in aqueous solutions. Our experiments show that the increase in magnitude of the charge of the HPAs increases their repulsive interactions and inhibits their aggregation in aqueous solutions. MD simulations were done to reveal the atomistic scale origins of SALR between HPAs. The short-range attractions result from water or proton-mediated hydrogen bonds between neighboring HPAs, whereas the long-range repulsions are due to the distributions of ions surrounding the HPAs.

Controlling the assembly of soft and deformable molecular aggregates into mesoscale structures is essential for understanding and developing a broad range of processes including rare earth extraction and cleaning of water, as well as for developing materials with unique properties. By combined synchrotron small- and wide-angle X-ray scattering with large-scale atomistic molecular dynamics simulations we analyze here a metalloamphiphile–oil solution that organizes on multiple length scales. The molecules associate into aggregates, and aggregates flocculate into meso-ordered phases. Our study demonstrates that dipolar interactions, centered on the amphiphile headgroup, bridge ionic aggregate cores and drive aggregate flocculation. By identifying specific intermolecular interactions that drive mesoscale ordering in solution, we bridge two different length scales that are classically addressed separately. Our results highlight the importance of individual intermolecular interactions in driving mesoscale ordering.

Spherical nucleic acid (SNA) nanostructures assemble into a large variety of well-defined crystalline superlattices viaDNA-directed hybridization. Crystallities of SNA with various shapes emerge during the assembly process, which coalesce during coarsening, leading to polycrystalline materials. Here, we investigate the growth dynamics of SNAs into body-centered cubic superlattices and the coalescence of SNA aggregates using a colloidal model formulated from the competition of electrostatic core repulsions and localized DNA hybridization attractions. We find that the growth law of isolated SNA crystallities is well-described by the power law t1/2, in agreement with experimental observations. At later times, coalescence slows the growth dynamics considerably and is dependent on the orientational mismatch (misorientation angle) of the coalescing crystallites. Molecular dynamics simulations show that the misorientation angle decreases continually during the coalescence, which is a signature of the grain rotation induced coalescence mechanism. This mechanism is followed by the coarsening of a “neck” that develops at the boundary between the coalescing crystallites. Remarkably, we find faster coalescence dynamics for larger SNAs compared to smaller SNAs due to their enhanced surface diffusion, which more effectively reduces curvature at the boundary of two superlattices. These findings provide fundamental insight into the relationship between nanoparticle surface chemistry and its crystallite growth and coalescence.

The radial distribution of monovalent cations surrounding spherical nucleic acid–Au nanoparticle conjugates (SNA-AuNPs) is determined by in situsmall-angle x-ray scattering (SAXS) and classical density functional theory (DFT) calculations. Small differences in SAXS intensity profiles from SNA-AuNPs dispersed in a series of solutions containing different monovalent ions (Na+, K+, Rb+, or Cs+) are measured. Using the “heavy ion replacement” SAXS (HIRSAXS) approach, we extract the cation-distribution-dependent contribution to the SAXS intensity and show that it agrees with DFT predictions. The experiment–theory comparisons reveal the radial distribution of cations as well as the conformation of the DNA in the SNA shell. The analysis shows an enhancement to the average cation concentration in the SNA shell that can be up to 15-fold, depending on the bulk solution ionic concentration. The study demonstrates the feasibility of HIRSAXS in probing the distribution of monovalent cations surrounding nanoparticles with an electron dense core (e.g., metals).

How molecular chirality manifests at the nano- to macroscale has been a scientific puzzle since Louis Pasteur discovered biochirality. Chiral molecules assemble into meso-shapes such as twisted and helical ribbons, helicoidal scrolls (cochleates), or möbius strips (closed twisted ribbons). Here we analyze self-assembly for a series of amphiphiles, Cn-K, consisting of an ionizable amino acid [lysine (K)] coupled to alkyl tails with n= 12, 14, or 16 carbons. This simple system allows us to probe the effects of electrostatic and van der Waals interactions in chiral assemblies. Small/wide-angle X-ray scattering (SAXS/WAXS) reveals that at low pH, where the headgroups are ionized (+1), C16-K forms high aspect ratio, planar crystalline bilayers. Molecular dynamics (MD) simulations reveal that tilted tails of the bilayer leaflets are interdigitated. SAXS shows that, with increasing salt concentration, C16-K molecules assemble into cochleates, whereas at elevated pH (reduced degree of ionization), helices are observed for all Cn-K assemblies. The shape selection between helices and scrolls is explained by a membrane energetics model. The nano- to meso-scale structure of the chiral assemblies can be continuously controlled by solution ionic conditions. Overall, our study represents a step toward an electrostatics-based approach for shape selection and nanoscale structure control in chiral assemblies.

Domain formation and control in pH-responsive amphiphilic polymer co-networks are studied theoretically. Two different molecular architectures of the polymer network are considered, depending on whether the pH-sensitive motif is borne by the hydrophobic or the hydrophilic monomer. When the hydrophobic polymer contains acidic groups, such chains form nanometric aggregates at acidic conditions, but they are found in a swollen state at alkaline pH. At intermediate pH, the nanoaggregation behavior of the hydrophobic polymer depends critically on the environment salt concentration. Moreover, our results indicate the presence of microphase separation into domains of swollen and aggregated hydrophobic chains. If the hydrophilic polymer is the ionizable component of the network, the nanoaggregation of hydrophobic monomers is weakly dependent on the pH and salt concentration, and except at very low volume fraction, the aggregate is the most probable conformation of the network in the entire range of pH and salt concentration studied. The two different hydrogels display quantitatively similar swelling transition and apparent pKa, but at the nanoscale, their behavior is qualitatively different. The spatial distribution of electric charge on the network as well as the local density of the different chemical species within the hydrogel can be controlled, as a function of pH and salt concentration, by the molecular architecture of the polymer network. These findings have relevance for applications in biomaterials and nanotechnology, in particular, in the design of oral delivery devices for the administration of hydrophobic drugs.

Decahedral morphology, with re-entrant surface modifications, is one of the common structures observed in nanoparticles. These motifs, although thermodynamically stable only at very small size ranges, have been experimentally observed to grow up to much larger sizes (100 nm to several micrometers). Whereas the surface energy plays an important role, the contributions of the elastic strain energy are nonnegligible at larger sizes and the effect of stress relaxation due to re-entrant surface faceting is poorly understood. In this article, the volumetric strain energy due to the disclination defect is computed using finite element analysis and the relaxation due to the formation of re-entrant surfaces is shown. Contrary to conventional wisdom, the disclination strain energy is shown to be a nontrivial function of the geometry and in general increases with increasing aspect ratio. The computed strain energies also result in approximately 50% increase in the stability regime than the previously reported results obtained using thermodynamical analysis. Finally, finite element analyses are utilized to explain the commonly observed defect configurations and compute the internal rigid body rotations in these particles.

Coassembled molecular structures are known to exhibit a large variety of geometries and morphologies. A grand challenge of self-assembly design is to find techniques to control the crystal symmetries and overall morphologies of multicomponent systems. By mixing +3 and −1 ionic amphiphiles, we assemble crystalline ionic bilayers in a large variety of geometries that resemble polyhedral cellular crystalline shells and archaea wall envelopes. We combine TEM with SAXS and WAXS to characterize the coassembled structures from the mesoscopic to nanometer scale. The degree of ionization of the amphiphiles and their intermolecular electrostatic interactions are controlled by varying pH. At low and high pH values, we observe closed, faceted vesicles with two-dimensional hexagonal molecular arrangements, and at intermediate pH, we observe ribbons with rectangular-C packing. Furthermore, as pH increases, we observe interdigitation of the bilayer leaflets. Accurate atomistic molecular dynamics simulations explain the pH-dependent bilayer thickness changes and also reveal bilayers of hexagonally packed tails at low pH, where only a small fraction of anionic headgroups is charged. Coarse-grained simulations show that the mesoscale geometries at low pH are faceted vesicles where liquid-like edges separate flat crystalline domains. Our simulations indicate that the curved-to-polyhedral shape transition can be controlled by tuning the tail density in regions where sharp bends can form the polyhedral edges. In particular, the pH acts to control the overall morphology of the ionic bilayers by changing the local crystalline order of the amphiphile tails.

Polyvalent oligonucleotide-functionalized gold nanoparticles are remarkably stable in a cellular environment against degradation by nucleases, a property that was recently attributed to the local high concentration of mono- and divalent ions. To evaluate this hypothesis in more detail, we investigate the composition of the ion cloud around spherical nanoparticles that are functionalized by stiff, highly charged polyelectrolyte chains by means of classical density functional theory and molecular dynamics simulations. We present a cell model that includes ligands explicitly and both applies over the entire relevant parameter space and is in excellent quantitative agreement with simulations. We study the ion cloud for varying oligonucleotide grafting densities and bulk ionic concentrations, as well as different sizes of nanoparticles and chains, and distinguish a parameter regime where many-body interactions between the ligands have a dominant effect on the local environment. For small particles with high oligonucleotide surface densities, we find strongly enhanced local salt concentrations, a large radial component of the electric field between the ligands, and a pronounced localization of divalent ions near the surface of the nanoparticle, thus providing multiple supporting arguments for the hypothesis.

Using coarse-grained molecular dynamics simulations, we investigate the surface patterns of charged end-group ligands attached to faceted nanoparticles. A competition between electrostatic repulsion and hydrophobic ligand−ligand attraction leads to the formation of a number of different conformations of the ligand coatings. The most prominent conformation in icosahedral nanoparticles is a ridgelike structure that makes their surfaces highly anisotropic. Meanwhile, bundles seem more prominent than ridges for tetrahedral, cubic, octahedral, and dodecahedral nanoparticles of diameters comparable to the chain length. The applicability of the Debye−Huckel theory to describe the ridges is confirmed by comparing simulations with explicit ion simulations. We argue that a tunable ligand-coating pattern can be used as a simple and robust tool for achieving direction-dependent interactions between nanoparticles and provide control of their assembly into composite materials with a desired symmetry.

This paper describes the use of 1H NMR spectroscopy to measure the equilibrium constants for the solution-phase binding of two para-substituted aniline molecules (R-An), p-methoxyaniline (MeO-An) and p-bromoaniline (Br-An), to colloidal 4.1 nm CdSe quantum dots (QDs). Changes in the chemical shifts of the aromatic protons located ortho to the amine group on R-An were used to construct a binding isotherm for each R-An/QD system. These isotherms fit to a Langmuir function to yield Ka, the equilibrium constant for binding of the R-An ligands to the QDs; Ka≈ 150 M−1and ΔGads≈ −19 kJ/mol for both R = MeO and R = Br. 31P NMR indicates that the native octylphosphonate ligands, which, by inductively coupled plasma atomic emission spectroscopy, cover 90% of the QD surface, are not displaced upon binding of R-An. The MeO-An ligand quenches the photoluminescence of the QDs at much lower concentrations than does Br-An; the observation, therefore, that Ka,MeO-An≈ Ka,Br-Anshows that this difference in quenching efficiencies is due solely to differences in the nature of the electronic interactions of the bound R-An with the excitonic state of the QD.

We report a GPU implementation in HOOMD Blue of long-range electrostatic interactions based on the orientation-averaged Ewald sum scheme, introduced by Yakub and Ronchi (J. Chem. Phys.2003, 119, 11556). The performance of the method is compared to an optimized CPU version of the traditional Ewald sum available in LAMMPS, in the molecular dynamics of electrolytes. Our GPU implementation is significantly faster than the CPU implementation of the Ewald method for small to a sizable number of particles (∼105). Thermodynamic and structural properties of monovalent and divalent hydrated salts in the bulk are calculated for a wide range of ionic concentrations. An excellent agreement between the two methods was found at the level of electrostatic energy, heat capacity, radial distribution functions, and integrated charge of the electrolytes.

Clusters of charged nanoparticles in aqueous solutions are analyzed via molecular dynamics simulations. We simulate a two-dimensional system consisting of charged nanoparticles and their corresponding monovalent counterions, with no added salt. The effective pair potentials (EPPs) among these ions are obtained after contracting the water molecules from a full three-dimensional bulk model that explicitly includes the solvent. The dressed interaction site theory (DIST) allows us to adjust the dielectric constant of the solvent to its experimental value and to separate the EPPs among the ions into their short-range and electrostatic (long-range) components. These effective potentials are basically invariant under different ionic concentrations, and the short-range components of those involving at least one nanoparticle are almost independent of the nanoparticle charge. We then use these potentials as the input in our simulations to study cluster formation for different nanoparticle charges at the McMillan−Mayer level of approximation. The structure of the clusters and their net charge (nanoparticles plus absorbed counterions) are also discussed.

We analyze the possibility of inducing surface micellization of hydrophobic and charged block copolymers by an oppositely charged surface using a two-state model with lateral correlations among adsorbed chains. The electrostatic attraction between the charged block and the charged surface induces diblock copolymer micellization on the surface at copolymer concentrations well below the critical micelle concentration in the bulk. We study systems with strong charge groups which have fixed charge densities and systems with weak charge groups which have solution-dependent degrees of ionizations. We analyze the effects of salt concentration, solution pH, surface charge density, polyelectrolyte block line charge density, surface tension of the hydrophobic block, and polymerization degrees of the blocks on the induced micellization. It is found that at low salt concentrations the number of chains per micelle does not significantly depend on the degree of polymerization of the charged block. The addition of salt increases the critical surface micelle concentration when the electrostatic attraction between the charged blocks and the surface dominates the electrostatic repulsion among adsorbed chains. At low salt concentration, the excluded volume has a minor effect on surface induced micelles for systems with strong charge groups. However, in systems with weak charge groups, where both the surface and block degrees of ionizations are determined self-consistently as a function of pH, the excluded volume decreases the pH effect on the polyelectrolyte degree of ionization at surfaces.