Modeling the Crystallization of Spherical Nucleic Acid Nanoparticle Conjugates with Molecular Dynamics Simulations

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Bottom-up assemblies of plasmonic nanoparticles exhibit unique optical effects such as tunable reflection, optical cavity modes, and tunable photonic resonances. Here, we compare detailed simulations with experiment to explore the effect of structural inhomogeneity on the optical response in DNA-gold nanoparticle superlattices. In particular, we explore the effect of background environment, nanoparticle polydispersity (>10%), and variation in nanoparticle placement (∼5%). At volume fractions less than 20% Au, the optical response is insensitive to particle size, defects, and inhomogeneity in the superlattice. At elevated volume fractions (20% and 25%), structures incorporating different sized nanoparticles (10-, 20-, and 40-nm diameter) each exhibit distinct far-field extinction and near-field properties. These optical properties are most pronounced in lattices with larger particles, which at fixed volume fraction have greater plasmonic coupling than those with smaller particles. Moreover, the incorporation of experimentally informed inhomogeneity leads to variation in far-field extinction and inconsistent electric-field intensities throughout the lattice, demonstrating that volume fraction is not sufficient to describe the optical properties of such structures. These data have important implications for understanding the role of particle and lattice inhomogeneity in determining the properties of plasmonic nanoparticle lattices with deliberately designed optical properties.T he rational arrangement of nanoparticles in multiple dimensions is a promising means for creating materials with novel properties not found in nature. Noble metal nanoparticles are interesting material building blocks due to their ability to amplify local fields by orders of magnitude and scatter light well below the diffraction limit. These efficient interactions with visible light are due to localized surface plasmon resonances (LSPRs), the collective oscillation of conduction electrons (1). Hierarchical arrangements of plasmonic nanoparticles have become the basis for colorimetric sensors (2, 3), subdiffraction limited waveguides (4), visible light metamaterials (5), and nanoscale lasing devices (6, 7), and the ability to adjust architecture in such materials has led to a wide variety of structures with tunable and unusual optical properties (8-12). Many of these technologies leverage the scalability and modularity of bottom-up assembly techniques, which use chemically synthesized colloidal nanoparticles as building blocks (13,14). Unfortunately, all nanoparticle assembly techniques result in materials with structural defects across multiple length scales, including imprecise particle placement, grain boundaries, and variation in crystallite size. In addition, the nanoparticles used in these systems are inherently inhomogeneous: varying in size, shape, and radius of curvature. Although the effects of inhomogeneity have been investigated at the individual nanoparticle level (15, 16), the effects of inhomogeneity on plasmonic assemblies are...

Section: Resultsmentioning

confidence: 99%

Defect tolerance and the effect of structural inhomogeneity in plasmonic DNA-nanoparticle superlattices

Ross

Blaber

et al. 2015

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“…Currently, it is believed that ssDNA-grafted particles form four different crystal structures (7,8). The primary control variables here are (i) the number of ssDNA grafted to the core, which determines the number of interaction sites, and (ii) the hydrodynamic radius of each colloid, which can be defined as the radius of the colloidal core plus the length of the monodisperse DNA chains grafted onto it.…”

Section: Modelmentioning

confidence: 99%

“…The CCM, based purely on enthalpies, is able to capture these trends (see Fig. 3A) through variations in the hydrodynamic size ratio of the particles including the DNA shells (r), and the ratio of the number of DNA per particle that are able to hybridize, the linker DNA number ratio (l) (5)(6)(7)(8). This model calculates the percent of DNA duplexes that could be formed for each particle in a binary crystal structure based on the number of complementary-type nearest neighbors, and number of particles in the unit…”

Section: Modelmentioning

confidence: 99%

“…DNA-grafted colloids | inverse design | nanostructures | crystal lattice predictions | evolutionary algorithm A topic of much interest in the current literature is the selfassembly of colloid particles multiply grafted with ssDNA molecules (1)(2)(3)(4)(5)(6)(7)(8)(9)(10). The typical experimental system consists of two types of colloids grafted with complementary ssDNA sequences.…”

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confidence: 99%

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Designing DNA-grafted particles that self-assemble into desired crystalline structures using the genetic algorithm

Srinivasan

Zhang

et al. 2013

In conventional research, colloidal particles grafted with singlestranded DNA are allowed to self-assemble, and then the resulting crystal structures are determined. Although this Edisonian approach is useful for a posteriori understanding of the factors governing assembly, it does not allow one to a priori design ssDNA-grafted colloids that will assemble into desired structures. Here we address precisely this design issue, and present an experimentally validated evolutionary optimization methodology that is not only able to reproduce the original phase diagram detailing regions of known crystals, but is also able to elucidate several previously unobserved structures. Although experimental validation of these structures requires further work, our early success encourages us to propose that this genetic algorithm-based methodology is a promising and rational materials-design paradigm with broad potential applications.DNA-grafted colloids | inverse design | nanostructures | crystal lattice predictions | evolutionary algorithm A topic of much interest in the current literature is the selfassembly of colloid particles multiply grafted with ssDNA molecules (1-10). The typical experimental system consists of two types of colloids grafted with complementary ssDNA sequences. Upon cooling, hybridization of the DNA occurs, crosslinking the colloids. Under the right conditions this cross-linking can facilitate the ordering of the colloids into crystal structures. The typical dimensions of colloids result in periodicities comparable to the wavelength of visible length, which have made them attractive for various emergent technologies, e.g., photonic bandgap materials. Classes of plasmonic, light-emitting, and catalytic metamaterials can be realized via the self-assembly of ssDNAgrafted colloids into specified 3D arrays.Although much work has examined the effects of temperature, DNA length, linker DNA groups, size of colloids, etc., on structure formation, it has been largely empirically driven. However, there has been some progress in theory and simulation on understanding this assembly process (5, 6, 11-13). The recent work of Starr and coworkers, for example, has emphasized the complicated phase and assembly behavior of these materials (11,12,14). Travesset and coworkers (5) and Olvera de la Cruz and coworkers (15) have used large-scale molecular dynamics simulations to study equilibrium aspects and the kinetics of self-assembly, including kinetic traps like gel formation. Crocker and coworker developed a quantitative model based on experimental studies to predict ssDNA-induced particle interactions, the driving force for self-assembly (16). Similarly, Frenkel and coworkers has also defined a general accurate theory of valence-limited colloidal interactions (17). In a similar vein, Mirkin and coworkers proposed a rule-based complementary contact model (CCM) to predict the formation of crystal structures by ssDNA-grafted colloids (7). This model was used to explain the four crystal structures experimentally observed.Althou...

“…In these systems, however, the identity of the atom and its bonding behavior cannot be independently controlled, limiting our ability to tune material properties at will. In contrast, when a nanoparticle is modified with a dense shell of upright, oriented DNA, it can behave as a programmable atom equivalent (PAE) (1, 2) that can be used to synthesize diverse crystal structures with independent control over composition, scale, and lattice symmetry (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14). The thermodynamic product of this crystallization process has been extensively studied by both experimental and theoretical means, and thus a series of design rules has been proposed and validated with a simple geometric model known as the complementary contact model (CCM).…”

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confidence: 99%

Importance of the DNA “bond” in programmable nanoparticle crystallization

Macfarlane

Thaner

Brown

et al. 2014

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If a solution of DNA-coated nanoparticles is allowed to crystallize, the thermodynamic structure can be predicted by a set of structural design rules analogous to Pauling's rules for ionic crystallization. The details of the crystallization process, however, have proved more difficult to characterize as they depend on a complex interplay of many factors. Here, we report that this crystallization process is dictated by the individual DNA bonds and that the effect of changing structural or environmental conditions can be understood by considering the effect of these parameters on free oligonucleotides. Specifically, we observed the reorganization of nanoparticle superlattices using time-resolved synchrotron small-angle X-ray scattering in systems with different DNA sequences, salt concentrations, and densities of DNA linkers on the surface of the nanoparticles. The agreement between bulk crystallization and the behavior of free oligonucleotides may bear important consequences for constructing novel classes of crystals and incorporating new interparticle bonds in a rational manner.DNA materials | self assembly | nanostructure M aterials scientists have accomplished much by studying the way atoms and molecules crystallize. In these systems, however, the identity of the atom and its bonding behavior cannot be independently controlled, limiting our ability to tune material properties at will. In contrast, when a nanoparticle is modified with a dense shell of upright, oriented DNA, it can behave as a programmable atom equivalent (PAE) (1, 2) that can be used to synthesize diverse crystal structures with independent control over composition, scale, and lattice symmetry (3-14). The thermodynamic product of this crystallization process has been extensively studied by both experimental and theoretical means, and thus a series of design rules has been proposed and validated with a simple geometric model known as the complementary contact model (CCM). These rules allow one to predict the thermodynamically favored structure as the arrangement of particles that maximizes complementary contacts and therefore DNA hybridization (2, 6). These efforts have been very successful in predicting the thermodynamically favored product; recent studies have even demonstrated that PAEs can form single-crystal Wulff polyhedra that are analogous to those formed in atomic systems with the same crystallographic symmetry (15). However, the fact that there is a crystalline thermodynamic product does not mean that any choice of DNA and nanoparticles will result in crystalline systems in practice (3, 4). For example, crystallization has been observed for a relatively narrow class of PAEs (16) and in a manner that is primarily dependent upon the length of the DNA linker and temperature at which assembly occurs (8). Thus, absent from our understanding of these systems is a connection between the crystallization process and the properties of the DNA bonds that form the foundation of these structures.Here, we study the crystallization process and find t...