Chiral assemblies of pinwheel superlattices on substrates.

The unique topology and physics of chiral superlattices make their self-assembly from nanoparticles highly sought after yet challenging in regard to (meta)materials1-3. Here we show that tetrahedral gold nanoparticles can transform from a perovskite-like, low-density phase with corner-to-corner connections into pinwheel assemblies with corner-to-edge connections and denser packing. Whereas corner-sharing assemblies are achiral, pinwheel superlattices become strongly mirror asymmetric on solid substrates as demonstrated by chirality measures. Liquid-phase transmission electron microscopy and computational models show that van der Waals and electrostatic interactions between nanoparticles control thermodynamic equilibrium. Variable corner-to-edge connections among tetrahedra enable fine-tuning of chirality. The domains of the bilayer superlattices show strong chiroptical activity as identified by photon-induced near-field electron microscopy and finite-difference time-domain simulations. The simplicity and versatility of substrate-supported chiral superlattices facilitate the manufacture of metastructured coatings with unusual optical, mechanical and electronic characteristics.

Perovskite-type superlattices from lead halide perovskite nanocubes.

Atomically defined assemblies of dye molecules (such as H and J aggregates) have been of interest for more than 80 years because of the emergence of collective phenomena in their optical spectra1-3, their coherent long-range energy transport, their conceptual similarity to natural light-harvesting complexes4,5, and their potential use as light sources and in photovoltaics. Another way of creating versatile and controlled aggregates that exhibit collective phenomena involves the organization of colloidal semiconductor nanocrystals into long-range-ordered superlattices6. Caesium lead halide perovskite nanocrystals7-9 are promising building blocks for such superlattices, owing to the high oscillator strength of bright triplet excitons10, slow dephasing (coherence times of up to 80 picoseconds) and minimal inhomogeneous broadening of emission lines11,12. So far, only single-component superlattices with simple cubic packing have been devised from these nanocrystals13. Here we present perovskite-type (ABO3) binary and ternary nanocrystal superlattices, created via the shape-directed co-assembly of steric-stabilized, highly luminescent cubic CsPbBr3 nanocrystals (which occupy the B and/or O lattice sites), spherical Fe3O4 or NaGdF4 nanocrystals (A sites) and truncated-cuboid PbS nanocrystals (B sites). These ABO3 superlattices, as well as the binary NaCl and AlB2 superlattice structures that we demonstrate, exhibit a high degree of orientational ordering of the CsPbBr3 nanocubes. They also exhibit superfluorescence-a collective emission that results in a burst of photons with ultrafast radiative decay (22 picoseconds) that could be tailored for use in ultrabright (quantum) light sources. Our work paves the way for further exploration of complex, ordered and functionally useful perovskite mesostructures.

Solvent Isotherms and Structural Transitions in Nanoparticle Superlattice Assembly.

We introduce a Molecular Theory for Compressible Fluids (MOLT-CF) that enables us to compute free energies and other thermodynamic functions for nanoparticle superlattices with any solvent content, including the dry limit. Quantitative agreement is observed between MOLT-CF and united-atom molecular dynamics simulations performed to assess the reliability and precision of the theory. Among other predictions, MOLT-CF shows that the amount of solvent within the superlattice decreases approximately linearly with its vapor pressure and that in the late stages of drying, solvent-filled voids form at lattice interstitials. Applied to single-component superlattices, MOLT-CF predicts fcc-to-bcc Bain transitions for decreasing vapor pressure and for increasing ligand length, both in agreement with experimental results. We explore the stability of other single-component phases and show that the C14 Frank-Kasper phase, which has been reported in experiments, is not a global free-energy minimum. Implications for precise assembly and prediction of multicomponent nanoparticle systems are discussed.

Exact Solution for Elastic Networks on Curved Surfaces.

The problem of characterizing the structure of an elastic network constrained to lie on a frozen curved surface appears in many areas of science and has been addressed by many different approaches, most notably, extending linear elasticity or through effective defect interaction models. In this Letter, we show that the problem can be solved by considering nonlinear elasticity in an exact form without resorting to any approximation in terms of geometric quantities. In this way, we are able to consider different effects that have been unwieldy or not viable to include in the past, such as a finite line tension, explicit dependence on the Poisson ratio, or the determination of the particle positions for the entire lattice. Several geometries with rotational symmetry are solved explicitly. Comparison with linear elasticity reveals an agreement that extends beyond its strict range of applicability. Implications for the problem of the characterization of virus assembly are also discussed.

Nanocomposite tectons as unifying systems for nanoparticle assembly.

Nanocomposite tectons (NCTs) are nanocomposite building blocks consisting of nanoparticle cores functionalized with a polymer brush, where each polymer chain terminates in a supramolecular recognition group capable of driving particle assembly. Like other ligand-driven nanoparticle assembly schemes (for example those using DNA-hybridization or solvent evaporation), NCTs are able to make colloidal crystal structures with precise particle organization in three dimensions. However, despite the similarity of NCT assembly to other methods of engineering ordered particle arrays, the crystallographic symmetries of assembled NCTs are significantly different. In this study, we provide a detailed characterization of the dynamics of hybridizations through universal (independent of microscopic details) parameters. We perform rigorous free energy calculations and identify the persistence length of the ligand as the critical parameter accounting for the differences in the phase diagrams of NCTs and other assembly methods driven by hydrogen bond hybridizations. We also report new experiments to provide direct verification for the predictions. We conclude by discussing the role of non-equilibrium effects and illustrating how NCTs provide a unification of the two most successful strategies for nanoparticle assembly: solvent evaporation and DNA programmable assembly.

Effect of Polymer Chain Length on the Superlattice Assembly of Functionalized Gold Nanoparticles.

We report on the assembly of gold nanoparticle (AuNPs) superlattices at the liquid/vapor interface and in the bulk of their suspensions. Interparticle distances in the assemblies are achieved on multiple length scales by varying chain lengths of surface grafted AuNPs by polyethylene glycol (PEG) with molecular weights in the range 2000-40,000 Da. Crystal structures and lattice constants in both 2D and 3D assemblies are determined by synchrotron-based surface-sensitive and small-angle X-ray scattering. Assuming knowledge of grafting density, we show that experimentally determined interparticle distances are adequately modeled by spherical brushes close to the θ point (Flory-Huggins parameter, χ≈12) for 2D superlattices at a liquid interface and a nonsolvent (χ = ∞) for the 3D dry superlattices.

Why large icosahedral viruses need scaffolding proteins.

While small single-stranded viral shells encapsidate their genome spontaneously, many large viruses, such as the herpes simplex virus or infectious bursal disease virus (IBDV), typically require a template, consisting of either scaffolding proteins or an inner core. Despite the proliferation of large viruses in nature, the mechanisms by which hundreds or thousands of proteins assemble to form structures with icosahedral order (IO) is completely unknown. Using continuum elasticity theory, we study the growth of large viral shells (capsids) and show that a nonspecific template not only selects the radius of the capsid, but also leads to the error-free assembly of protein subunits into capsids with universal IO. We prove that as a spherical cap grows, there is a deep potential well at the locations of disclinations that later in the assembly process will become the vertices of an icosahedron. Furthermore, we introduce a minimal model and simulate the assembly of a viral shell around a template under nonequilibrium conditions and find a perfect match between the results of continuum elasticity theory and the numerical simulations. Besides explaining available experimental results, we provide a number of predictions. Implications for other problems in spherical crystals are also discussed.

Assembly of nanocrystal clusters by solvent evaporation: icosahedral order and the breakdown of the Maxwell regime.

We carry out molecular dynamics simulations of N gold alkylthiolated nanocrystals (0 ≤ N ≤ 29) contained in liquid droplets of octane, nonane and decane coexisting with its vapor. The equilibrium structures that result when all the solvent dries up consist of highly symmetric nanocrystal clusters with different degrees of icosahedral order that are thoroughly characterized. We show that the relaxation times follow two regimes, a first for small nanocrystal packing fraction, dominated by the diffusion of vapor molecules (Maxwell regime, relaxation times independent of N) and another, for larger packing fractions, where the solvent diffuses through the cluster (with relaxation times growing like N2/3). We discuss the connection to the assembly of superlattices, prediction of lattice constants and evaporation models.

The hard sphere diameter of nanocrystals (nanoparticles).

The hard sphere diameter dHS of a nanocrystal (or nanoparticle) is a very important parameter that determines the nearest neighbor separation of their assembled structure, even in those situations where the nanocrystals have large deformations of the ligand shell that prevent them from being described as hard spheres. The parameter dHS is a function of the number of grafted ligands and critically depends on the maximum ligand grafting density σMax, which we calculate by three different methods for the 351 gold nanocrystals with the number of atoms between 38 and 4033. The use of dHS in the interpretation of experimental results is analyzed.

Ligand structure and adsorption free energy of nanocrystals on solid substrates.

We present an investigation on the absorption of alkylthiolated nanocrystals on a solid substrate. We calculate adsorption free energies and report a number of effects induced by the substrate. Nearest neighbor distances and bonding free energies are significantly different than for a free floating case, there is a weakening of bonding free energies among nanocrystals, and the adsorption is manifestly anisotropic, i.e., stronger along certain directions of the nanocrystal core. We contend that this last result accounts for the Bain transition (fcc → bcc) observed in experimental results. We report the presence of vortices induced by the substrate, which explain the increased nearest neighbor distance among nanocrystals, which is in excellent quantitative agreement with experimental results and with the predictions of the Orbifold Topological Model. Implications for the assembly of nanostructures and future experiments are also discussed.

Ground States of Crystalline Caps: Generalized Jellium on Curved Space.

We study the ground states of crystals on spherical surfaces. These ground states consist of positive disclination defects in structures spanning from flat and weakly curved caps to closed shells. Comparing two continuum theories and one discrete-lattice simulation, we first investigate the transition between defect-free caps to single-disclination ground states and show it to be continuous and symmetry breaking. Further, we show that ground states adopt icosahedral subgroup symmetries across the full range of curvatures, even far from the closure of complete shells. While superficially similar to other models of 2D "jellium" (e.g., superconducting disks and 2D Wigner crystals), the interplay between the free edge of caps and the non-Euclidean geometry of its embedding leads to nontrivial ground state behavior that is without counterpart in planar jellium models.

Superlattice assembly by interpolymer complexation.

We present a coarse grained model for a system where nanocrystals are functionalized with a polymer that is a hydrogen bond acceptor, such as polyethylene glycol (PEG), and are dispersed in a solution with a polymer whose monomers consist of a hydrogen bond donor, such as polyacrylic acid (PAA) at low pH (interpolymer complexation). We determine the minimum concentration of the polymer donor to induce aggregation and the structure and dynamics of the induced (fcc) superlattice. Our results are compared to previous and new experiments.

Many Body Effects and Icosahedral Order in Superlattice Self-Assembly.

We elucidate how nanocrystals "bond" to form ordered structures. For that purpose we consider nanocrystal configurations consisting of regular polygons and polyhedra, which are the motifs that constitute single component and binary nanocrystal superlattices, and simulate them using united atom models. We compute the free energy and quantify many body effects, i.e., those that cannot be accounted for by pair potential (two-body) interactions, further showing that they arise from coalescing vortices of capping ligands. We find that such vortex textures exist for configurations with local coordination number ≤6. For higher coordination numbers, vortices are expelled and nanocrystals arrange in configurations with tetrahedral or icosahedral order. We provide explicit formulas for the optimal separations between nanocrystals, which correspond to the minima of the free energies. Our results quantitatively explain the structure of superlattice nanocrystals as reported in experiments and reveal how packing arguments, extended to include soft components, predict ordered nanocrystal aggregation.

Calculation of critical nucleation rates by the persistent embryo method: application to quasi hard sphere models.

We study the crystal nucleation of the Weeks-Chandler-Andersen (WCA) model, using the recently introduced persistent embryo method (PEM). The method provides detailed characterization of pre-critical, critical and post-critical nuclei, as well as nucleation rates that compare favorably with those obtained using other methods (umbrella sampling, forward flux sampling or seeding). We further map our results to a hard sphere model allowing comparison with other existing predictions. Implications for experiments are also discussed.

Potential of mean force for two nanocrystals: Core geometry and size, hydrocarbon unsaturation, and universality with respect to the force field.

We present a detailed analysis of the interaction between two nanocrystals capped with ligands consisting of hydrocarbon chains by united atom molecular dynamics simulations. We analyze large cores (up to 10 nm in diameter) and ligands with unsaturated carbon bonds (oleic acid) and we investigate the accuracy of the computed potential of mean force by comparing different force fields. We also analyze the vortices that determine the bonding, including the case of asymmetric nanocrystals, and discuss effects related to the intrinsic anisotropy of the core. Overall our results are in agreement with the predictions of the recently proposed orbifold topological model.

Binary nanoparticle superlattices of soft-particle systems.

The solid-phase diagram of binary systems consisting of particles of diameter σA = σ and σB = γσ (γ ≤ 1) interacting with an inverse p = 12 power law is investigated as a paradigm of a soft potential. In addition to the diameter ratio γ that characterizes hard-sphere models, the phase diagram is a function of an additional parameter that controls the relative interaction strength between the different particle types. Phase diagrams are determined from extremes of thermodynamic functions by considering 15 candidate lattices. In general, it is shown that the phase diagram of a soft repulsive potential leads to the morphological diversity observed in experiments with binary nanoparticles, thus providing a general framework to understand their phase diagrams. Particular emphasis is given to the two most successful crystallization strategies so far: evaporation of solvent from nanoparticles with grafted hydrocarbon ligands and DNA programmable self-assembly.

Nanoparticle Superlattices as Quasi-Frank-Kasper Phases.

I show that all phases reported experimentally in binary nanoparticle superlattices can be described as networks of disclinations in an ideal lattice of regular tetrahedra. A set of simple rules is provided to identify the different disclination types from the Voronoi construction, and it is shown that those disclinations completely screen the positive curvature of the ideal tetrahedral lattice. In this way, this study provides a generalization of the well-known Frank-Kasper phases to binary systems consisting of two types of particles, and with a more general type of disclinations, i.e., quasi-Frank-Kasper phases. The study comprises all strategies in nanoparticle self-assembly, whether driven by DNA or hydrocarbon ligands, and establishes the universal tendency of superlattices to develop icosahedral order, which is facilitated by the asymmetry of the particles. Besides its interest in predicting nanoparticle self-assembly, I discuss the implications for models of the glass transition, micelles of diblock polymers, and dendritic molecules, among many others.

Prediction of binary nanoparticle superlattices from soft potentials.

Driven by the hypothesis that a sufficiently continuous short-ranged potential is able to account for shell flexibility and phonon modes and therefore provides a more realistic description of nanoparticle interactions than a hard sphere model, we compute the solid phase diagram of particles of different radii interacting with an inverse power law potential. From a pool of 24 candidate lattices, the free energy is optimized with respect to additional internal parameters and the p-exponent, determining the short-range properties of the potential, is varied between p = 12 and p = 6. The phase diagrams contain the phases found in ongoing self-assembly experiments, including DNA programmable self-assembly and nanoparticles with capping ligands assembled by evaporation from an organic solvent. The resulting phase diagrams can be mapped quantitatively to existing experiments as a function of only two parameters: Nanoparticle radius ratio (γ) and softness asymmetry.

Differential dynamics of RAS isoforms in GDP- and GTP-bound states.

RAS subfamily proteins regulates cell growth promoting signaling processes by cycling between active (GTP-bound) and inactive (GDP-bound) states. Different RAS isoforms, though structurally similar, exhibit functional specificity and are associated with different types of cancers and developmental disorders. Understanding the dynamical differences between the isoforms is crucial for the design of inhibitors that can selectively target a particular malfunctioning isoform. In this study, we provide a comprehensive comparison of the dynamics of all the three RAS isoforms (HRAS, KRAS, and NRAS) using extensive molecular dynamics simulations in both the GDP- (total of 3.06 µs) and GTP-bound (total of 2.4 µs) states. We observed significant differences in the dynamics of the isoforms, which rather interestingly, varied depending on the type of the nucleotide bound and the simulation temperature. Both SwitchI (Residues 25-40) and SwitchII (Residues 59-75) differ significantly in their flexibility in the three isoforms. Furthermore, Principal Component Analysis showed that there are differences in the conformational space sampled by the GTP-bound RAS isoforms. We also identified a previously unreported pocket, which opens transiently during MD simulations, and can be targeted to regulate nucleotide exchange reaction or possibly interfere with membrane localization. Further, we present the first simulation study showing GDP destabilization in the wild-type RAS protein. The destabilization of GDP/GTP occurred only in 1/50 simulations, emphasizing the need of guanine nucleotide exchange factors (GEFs) to accelerate such an extremely unfavorable process. This observation along with the other results presented in this article further support our previously hypothesized mechanism of GEF-assisted nucleotide exchange.

Folding 19 proteins to their native state and stability of large proteins from a coarse-grained model.

We develop an intermediate resolution model, where the backbone is modeled with atomic resolution but the side chain with a single bead, by extending our previous model (Proteins (2013) DOI: 10.1002/prot.24269) to properly include proline, preproline residues and backbone rigidity. Starting from random configurations, the model properly folds 19 proteins (including a mutant 2A3D sequence) into native states containing ß sheet, α helix, and mixed α/ß. As a further test, the stability of H-RAS (a 169 residue protein, critical in many signaling pathways) is investigated: The protein is stable, with excellent agreement with experimental B-factors. Despite that proteins containing only α helices fold to their native state at lower backbone rigidity, and other limitations, which we discuss thoroughly, the model provides a reliable description of the dynamics as compared with all atom simulations, but does not constrain secondary structures as it is typically the case in more coarse-grained models. Further implications are described.