[Show abstract][Hide abstract] ABSTRACT: Shape-controlled synthesis of gold nanoparticles generally involves the use of surfactants, typically cetyltrimethylammonium (CTAX, X = Cl(-) , Br(-) ), to regulate the nucleation growth process and to obtain colloidally stable nanoparticles. The surfactants adsorb on the nanoparticle surface making further functionalization difficult and therefore limit their use in many applications. Herein, the influence of CTAX on nanoparticle sensitivity to local dielectric environment changes is reported. It is shown, both experimentally and theoretically, that the CTAX bilayer significantly reduces the refractive index (RI) sensitivity of anisotropic gold nanoparticles such as nanocubes and concave nanocubes, nanorods, and nanoprisms. The RI sensitivity can be increased by up to 40% by removing the surfactant layer from nanoparticles immobilized on a solid substrate using oxygen plasma treatment. This increase compensates for the otherwise problematic decrease in RI sensitivity caused by the substrate effect. Moreover, the removal of the surfactants both facilitates nanoparticle biofunctionalization and significantly improves their catalytic properties. The strategy presented herein is a simple yet effective universal method for enhancing the RI sensitivity of CTAX-stabilized gold nanoparticles and increasing their potential as transducers in nanoplasmonic sensors, as well as in catalytic and biomedical applications.
Small 11/2015; DOI:10.1002/smll.201502449 · 8.37 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: For electrochemical device applications metal organic frameworks (MOFs) must exhibit suitable conduction properties. To this end, we have performed computational studies of intermolecular charge transfer in MOFs consisting of hexa-ZrIV nodes and tetratopic carboxylate linkers. This includes an examination of the electronic structure of linkers that are derived from tetraphenyl benzene 1, tetraphenyl pyrene 2, and tetraphenyl porphyrin 3 molecules. These results are used to determine charge transfer propensities in MOFs, within the framework of Marcus theory, including an analysis of the key parameters (charge transfer integral t, reorganization energy λ, and free energy change δG0) and evaluation of figures of merit for charge transfer based on the chemical structures of the linkers. This qualitative analysis indicates that delocalization of the HOMO/LUMO on terminal substituents increases t and decreases λ, while weaker binding to counterions decreases δG0, leading to better charge transfer propensity. Subsequently, we study hole transfer in the linker 2 containing MOFs, NU-901 and NU-1000, in detail and describe mechanisms (hopping and superexchange) that may be operative under different electrochemical conditions. Comparisons with experiment are provided where available. On the basis of the redox and catalytic activity of nodes and linkers, we propose three possible schemes for constructing electrochemical devices for catalysis. We believe that the results of this study will lay the foundation for future experimental work on this topic.
The Journal of Physical Chemistry C 10/2015; 119(43):151019083356009. DOI:10.1021/acs.jpcc.5b06065 · 4.77 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Chemical bonds are a key determinant of the structure and properties of a material. Thus, rationally designing arbitrary materials requires complete control over the bond. While atomic bonding is dictated by the identity of the atoms, nanoparticle superlattice engineering, where nanoparticle "atoms" are held together by DNA "bonds", offers a route to design crystal lattices in a way that nature cannot: through altering the oligonucleotide bond. Herein, the use of RNA, as opposed to DNA, is explored by synthesizing superlattices in which nanoparticles are bonded by DNA/DNA, RNA/RNA, and DNA/RNA duplexes. By moving beyond nanoparticle superlattices assembled only with DNA, a new degree of freedom is introduced, providing programmed responsiveness to enzymes and greater bond versatility. Therefore, the oligonucleotide bond can have programmable function beyond dictating the structure of the material and moves nanoparticle superlattices closer to naturally occurring biomaterials, where the line between structural and functional elements is blurred.
Journal of the American Chemical Society 10/2015; 137(42). DOI:10.1021/jacs.5b07908 · 12.11 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Two complementary small molecule-DNA hybrid (SMDH) building blocks have been combined to form well-defined supramolecular cage dimers at DNA concentrations as high as 102 μM, made possible by combining a flexible small-molecule core and three DNA arms of moderate lengths (<20 base pairs). These results were successfully modeled by coarse-grained molecular dynamics (CGMD) simulations, which also reveal that the formation of ill-defined networks in the case of longer DNA arms can be significantly biased by the presence of deep kinetic traps. Notably, melting point studies revealed that cooperative melting behavior can be used as a means to distinguish the relative propensities for dimer vs network formation from complimentary fSMDH3 components: sharp, enhanced melting transitions were observed for assemblies that result mostly in cage dimers while no cooperative melting behavior was observed for assemblies that form ill-defined networks.
Journal of the American Chemical Society 09/2015; 137(41). DOI:10.1021/jacs.5b08678 · 12.11 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Myotonic Dystrophy 1 (DM1) is a genetic disease caused by expansion of CTG repeats in DNA. Once transcribed, these repeats form RNA hairpins with repeating 1×1 nucleotide UU internal loop motifs, r(CUG)n, which attract muscleblind-like 1 (MBNL1) protein leading to the disease. In DM1 CUG can be repeated thousands of times, so these structures are intractable to characterization using structural biology. However, inhibition of MBNL1-r(CUG)n binding requires a detailed analysis of the 1×1 UU internal loops. In this contribution we employ regular and umbrella sampling molecular dynamics (MD) simulations to describe the structural and thermodynamic properties of 1×1 UU internal loops. Calculations were run on a reported crystal structure and a designed system, which mimics an infinitely long RNA molecule with continuous CUG repeats. Two-dimensional (2D) potential of mean force (PMF) surfaces were created by umbrella sampling, and the discrete path sampling (DPS) method was utilized to investigate the energy landscape of 1×1 UU RNA internal loops, revealing that 1×1 UU base pairs are dynamic and strongly prefer the anti–anti conformation. Two 2D PMF surfaces were calculated for the 1×1 UU base pairs, revealing several local minima and three syn–anti ↔ anti–anti transformation pathways. Although at room temperature the syn–anti ↔ anti–anti transformation is not observed on the MD time scale, one of these pathways dominates the dynamics of the 1×1 UU base pairs in temperature jump MD simulations. This mechanism has now been treated successfully using the DPS approach. Our results suggest that local minima predicted by umbrella sampling calculations could be stabilized by small molecules, which is of great interest for future drug design. Furthermore, distorted GC/CG conformations may be important in understanding how MBNL1 binds to RNA CUG repeats. Hence we provide new insight into the dynamic roles of RNA loops and their contributions to presently incurable diseases.
Journal of Chemical Theory and Computation 08/2015; 11(10). DOI:10.1021/acs.jctc.5b00728 · 5.50 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Plasmonic near fields, wherein light is magnified and focused within nanoscale volumes, are utilized in a broad array of technologies including optoelectronics, catalysis, and sensing. Within these nanoscale cavities, increases in temperature are expected and indeed have been demonstrated. Heat generation can be beneficial or detrimental for a given system or technique, but in either case it is useful to have knowledge of local temperatures. Surface-enhanced Raman spectroscopy (SERS), potentially down to the limit of single-molecule (SM) detection, has been suggested as a viable route for measuring nanoscale temperatures through simultaneous collection of Stokes and anti-Stokes SER scattering, as the ratio of their intensities is related to the Boltzmann distribution. We have rigorously verified SM detection in anti-Stokes SERS of rhodamine 6G on aggregated Ag nanoparticles using the isotopologue method. We observe a broad distribution in the ratio of anti-Stokes and Stokes signal intensities among SM events. An equivalent distribution in high-coverage, single-aggregate SERS suggests that the observed variance is not a SM phenomenon. We find that the variance is instead caused by a combination of local heating differences among hot spots as well as variations in the near-field strength as a function of frequency, effectively causing nonequivalent enhancement factors (EFs) for anti-Stokes and Stokes scattering. Additionally, we demonstrate that dark-field scattering cannot account for the frequency dependence of the optical near field. Finite-difference time-domain simulations for nanoparticle aggregates predict a significant wavelength dependence to the ratio of anti-Stokes/Stokes EFs, confirming that the observed variation in this ratio has strong nonthermal contributions. Finally, we outline the considerations that must be addressed in order to accurately evaluate local temperatures using SERS.
The Journal of Physical Chemistry C 08/2015; 119(36):150825051053001. DOI:10.1021/acs.jpcc.5b08054 · 4.77 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Many transcriptional activators act at a distance from core promoter elements and work by recruiting RNA polymerase through protein-protein interactions. We show here how the prokaryotic regulatory protein CueR both represses and activates transcription by differentially modulating local DNA structure within the promoter. Structural studies reveal that the repressor state slightly bends the promoter DNA, precluding optimal RNA polymerase-promoter recognition. Upon binding a metal ion in the allosteric site, CueR switches into an activator conformation. It maintains all protein-DNA contacts but introduces torsional stresses that kink and undertwist the promoter, stabilizing an A-form DNA–like conformation. These factors switch on and off transcription by exerting dynamic control of DNA stereochemistry, reshaping the core promoter and making it a better or worse substrate for polymerase.
[Show abstract][Hide abstract] ABSTRACT: 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.
Proceedings of the National Academy of Sciences 08/2015; 112(33):10292-10297. DOI:10.1073/pnas.1513058112 · 9.67 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The properties of nanoparticle superstructures depend on many factors, including the structural metrics of the nanoparticle superstructure (particle diameter, interparticle distances, etc.). Here, we introduce a family of gold-binding peptide conjugate molecules that can direct nanoparticle assembly, and we describe how these molecules can be systematically modified to adjust the structural metrics of linear double-helical nanoparticle superstructures. 12 new peptide conjugates are prepared via linking a gold-binding peptide, AYSSGAPPMPPF (PEPAu), to a hydrophobic aliphatic tail. The peptide conjugates have 1, 2, or 3 PEPAu head groups and a C12, C14, C16, or C18 aliphatic tail. The soft assembly of these peptide conjugates was studied using transmission electron microscopy (TEM), atomic force microscopy (AFM), and infrared (IR) spectroscopy. Several peptide conjugates assemble into 1-D twisted fibers having measurable structural parameters such as fiber width, thickness, and pitch that can be systematically varied by adjusting the aliphatic tail length and number of peptide head groups. The linear soft assemblies serve as structural scaffolds for arranging gold nanoparticles into double-helical superstructures, which are examined via TEM. The pitch and interparticle distances of the gold nanoparticle double helices correspond to the underlying metrics of the peptide conjugate soft assemblies, illustrating that designed peptide conjugate molecules can be used to not only direct the assembly of gold nanoparticles but also control the metrics of the assembled structure.
[Show abstract][Hide abstract] ABSTRACT: Correction for 'Plasmonics in the ultraviolet with the poor metals Al, Ga, In, Sn, Tl, Pb, and Bi' by Jeffrey M. McMahon et al., Phys. Chem. Chem. Phys., 2013, 15, 5415-5423. This journal is
[Show abstract][Hide abstract] ABSTRACT: Understanding the atomistic mechanisms of carbon structure formation during templated multi-step
carbonization is very important for further optimization of carbon fiber mechanical properties. Here with
use of reactive force field molecular dynamics we have elucidated the mechanism driving double-walled
carbon nanotube- and graphite nanoparticle-based in situ templating of polyacrylonitrile derived fibers.
Depending on carbonization temperature, the mechanism involves either physisorption (physical templating)
or chemisorption (chemical templating) of the fiber medium to the template surface. In either
case, strong interaction between template and medium leads to the production of aligned structures that
are more robust for nanotubes than graphite. We provide a unique analysis of atomistic simulations that
enables quantitative comparison of templating results with the relevant electron diffraction data
[Show abstract][Hide abstract] ABSTRACT: We report a template-based technique for the preparation of solution-dispersible nanorings composed of Au, Ag, Pt, Ni, and Pd with control over outer diameter (60–400 nm), inner diameter (25–230 nm), and height (40 nm to a few microns). Systematic and independent control of these parameters enables fine-tuning of the three characteristic localized surface plasmon resonance modes of Au nanorings and the resulting solution-based extinction spectra from the visible to the near-infrared. This synthetic approach provides a new pathway for solution-based investigations of surfaces with negative curvature.
[Show abstract][Hide abstract] ABSTRACT: Weak inter-filament van der Waals interactions are potentially a significant roadblock in the development of carbon nanotube (CNT) and graphene-based nanocomposites. Chemical functionalization is envisioned as a means of introducing stronger intermolecular interactions at nanoscale interfaces which, in turn, could enhance composite strength. Here we measure the adhesive energy of CNT-graphite interfaces functionalized with various coverages of arylpropionic acid. In situ peeling experiments conducted within a scanning electron microscope show significantly larger adhesive energies compared to previously obtained measurements for unfunctionalized surfaces (Roenbeck et al., ACS Nano 2014). Surprisingly, however, adhesive energy measurements are significantly higher when both surfaces have intermediate coverages than when one surface is densely functionalized. Atomistic simulations reveal a novel functional group interdiffusion mechanism, which arises for intermediate coverages in the presence of water. This interdiffusion is not observed when one surface is densely functionalized, resulting in energy trends that correlate with those observed in experiments. This unique intermolecular interaction mechanism, combined with the integrated experimental-computational approach presented here, provides significant insights for use in the development of next-generation nanocomposites.
[Show abstract][Hide abstract] ABSTRACT: Control of both photonic and plasmonic coupling in a single optical device represents a challenge due to the distinct length scales that must be manipulated. Here, we show that optical metasurfaces with such control can be constructed using an approach that combines top-down and bottom-up processes, wherein gold nanocubes are assembled into ordered arrays via DNA hybridization events onto a gold film decorated with DNA-binding regions defined using electron beam lithography. This approach enables one to systematically tune three critical architectural parameters: (1) anisotropic metal nanoparticle shape and size, (2) the distance between nanoparticles and a metal surface, and (3) the symmetry and spacing of particles. Importantly, these parameters allow for the independent control of two distinct optical modes, a gap mode between the particle and the surface and a lattice mode that originates from cooperative scattering of many particles in an array. Through reflectivity spectroscopy and finite-difference time-domain simulation, we find that these modes can be brought into resonance and coupled strongly. The high degree of synthetic control enables the systematic study of this coupling with respect to geometry, lattice symmetry, and particle shape, which together serve as a compelling example of how nanoparticle-based optics can be useful to realize advanced nanophotonic structures that hold implications for sensing, quantum plasmonics, and tunable absorbers.
[Show abstract][Hide abstract] ABSTRACT: We examine the role played by surface structure and passivation in thermal transport at semiconductor/organic interfaces. Such interfaces dominate thermal transport in semiconductor nanomaterials owing to material dimensions much smaller than the bulk phonon mean free path. Utilizing reverse non-equilibrium molecular dynamics simulations, we calculate the interfacial thermal conductance (G) between a hexane solvent and chemically passivated, wurtzite CdSe surfaces. In particular, we examine the dependence of G on the CdSe slab thickness, the particular exposed crystal facet, and the extent of surface passivation. Our results indicate a non-monotonic dependence of G on ligand grafting density, with interfaces generally exhibiting higher thermal conductance for increasing surface coverage up to ~0.08 ligands/Å^2 and decreasing for still higher coverages. By analyzing orientational ordering and solvent penetration into the ligand layer, we show that a balance of competing effects is responsible for this non-monotonic dependence. Although the various unpassivated CdSe surfaces exhibit similar G values, the crystal structure of an exposed facet nevertheless plays an important role in determining the interfacial thermal conductance of passivated surfaces, as the density of binding sites on a surface determines the ligand grafting densities that may ultimately be achieved. We demonstrate that surface passivation can increase G relative to a bare surface by roughly an order of magnitude, and that for a given extent of passivation, thermal conductance can vary by up to a factor of ~2 between different surfaces, suggesting that appropriately tailored nanostructures may direct heat flow in an anisotropic fashion for interface-limited thermal transport.
[Show abstract][Hide abstract] ABSTRACT: We explore localized surface plasmon resonances in small (5–30 nm radius) aluminum and silver nanoparticles using classical electrodynamics simulations, focusing on radiative (far-field scattering) effects and the unique characteristics of aluminum as a plasmonic material. In Al spheres, higher-order plasmon resonances (e.g. quadrupoles) are significant at smaller sizes (>15 nm) than in Ag spheres. Additionally, although the plasmon width is minimized at a radius of about 15 nm for both materials, the Al plasmon linewidth (~1.4 eV) for the dipole mode is much larger than that observed in Ag (~0.3 eV). The radiative contribution to damping dominates over non-radiative effects for small (5–20 nm) Al spheres (>95%) whereas for similar size Ag spheres damping is almost entirely attributed to the bulk dielectric function (non-radiative). For Al nanorods the linewidths can be narrowed by increasing aspect ratio such that for an aspect ratio of 4.5, the overall Al (0.75 eV) linewidth is reasonably close to that of the same size Ag rod (0.35 eV). This narrowing arises from frequency dispersion in the real part of the Al dielectric function, and is associated with a 65% (1.5 to 0.5 eV) decrease in the radiative contribution to the linewidth for Al. Concurrently, an increase in the non-radiative width occurs as the aspect ratio increases and the plasmon tunes to the red. This demonstrates that anisotropy can be used as a parameter for controlling Al plasmon dephasing where the composition of the plasmon linewidth (radiative or non-radiative) can be tailored with aspect ratio. Overall, these data suggest that localized surface plasmon resonance dephasing mechanisms in Al nanostructures are inherently different from those in the noble metals, which could allow for new applications of plasmonic materials, tunable plasmon lifetimes, and new physics to be observed.
Journal of Physics D Applied Physics 05/2015; 48(18). DOI:10.1088/0022-3727/48/18/184004 · 2.72 Impact Factor