[show abstract][hide abstract] ABSTRACT: Spherical nucleic acid (SNA) nanostructures assemble into a large variety of well-defined crystalline superlattices via DNA-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 t(1/2), 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.
[show abstract][hide abstract] ABSTRACT: Chemically interfacing the inert basal plane of graphene with other materials has limited the development of graphene-based catalysts, composite materials, and devices. Here, we overcome this limitation by chemically activating epitaxial graphene on SiC(0001) using atomic oxygen. Atomic oxygen produces epoxide groups on graphene, which act as reactive nucleation sites for zinc oxide nanoparticle growth using the atomic layer deposition precursor diethyl zinc. In particular, exposure of epoxidized graphene to diethyl zinc abstracts oxygen, creating mobile species which diffuse on the surface to form metal oxide clusters. This mechanism is corroborated with a combination of scanning probe microscopy, Raman spectroscopy, and density functional theory, and can likely be generalized to a wide variety of related surface reactions on graphene.
Journal of the American Chemical Society 11/2013; · 10.68 Impact Factor
[show abstract][hide abstract] ABSTRACT: The photochemical reactions of eleven synthetic DNA hairpins possessing a single TT step either in a base-paired stem or in a hexanucleotide linker have been investigated. The major reaction products have been identified as the cis-syn (2 + 2) adduct and the (6 - 4) adduct on the basis of their spectroscopic properties including 1D and 2D NMR spectra, UV spectra and stability or instability to photochemical cleavage. Product quantum yields and ratios determined by HPLC analysis allow the behaviour of the eleven hairpins to be placed into three groups: Group I in which the (2 + 2) adduct is the major product, as is usually the case for DNA, Group II in which comparable amounts of (2 + 2) and (6 - 4) adducts are formed, and Group III in which the major product is the (6 - 4) adduct. The latter behaviour is without precedent in natural or synthetic DNA and appears to be related to the highly fluxional structures of the hairpin reactants. Molecular dynamics simulation of ground state conformations provides quantum yields and product ratios calculated using a single parameter model that are in reasonable agreement with most of the experimental results. Factors which may influence the observed product ratios are discussed.
Photochemical and Photobiological Sciences 11/2013; · 2.92 Impact Factor
[show abstract][hide abstract] ABSTRACT: Epsilon-near-zero behavior and an optically metallic response are predicted using electrodynamics simulations in superlattices comprising silver nanoparticles. Programmable DNA-mediated assembly is used to synthesize both silver and binary silver-gold nanoparticle superlattices, which are characterized using small-angle X-ray scattering, transmission electron microscopy, and elemental mapping.
[show abstract][hide abstract] ABSTRACT: The mechanism of self-assembly of 140 peptide amphiphiles (PAs) to give nanofiber structures was investigated using a coarse-grained method to quantitatively determine whether the assembly process involves discrete intermediates or is a continuous process. Two novel concepts are introduced for this analysis: a cluster analysis of the time dependence of PA assembly, and use of the fraction of native contacts as reaction coordinates for characterizing thermodynamic functions during assembly. The cluster analysis of the assembly kinetics demonstrates that a pillar-like intermediate state is formed before the final cylindrical semi-fiber structure. We also find that head-group assembly occurs on a much shorter time scale than tail group assembly. A 2D free-energy landscape with respect to the fraction of native contacts was calculated and the pillar-like intermediate structure is also found, with free energies about 1.2 kcal/mol higher than the final state. Although this intermediate state exists for only hundreds of ns, the PA self-assembly process can be recognized as involving two steps: (a) transition from the disordered state to the noncylindrical pillar-like intermediate, (b) pillar-like to final semi-fiber transition. These results are important to the further design of PAs as functional nanostructures.
The Journal of Physical Chemistry B 10/2013; · 3.61 Impact Factor
[show abstract][hide abstract] ABSTRACT: Semiconducting carbon nanotubes promise a broad range of potential applications in optoelectronics and imaging, but their photon-conversion efficiency is relatively low. Quantum theory suggests that nanotube photoluminescence is intrinsically inefficient because of low-lying 'dark' exciton states. Here we demonstrate the significant brightening of nanotube photoluminescence (up to 28-fold) through the creation of an optically allowed defect state that resides below the predicted energy level of the dark excitons. Emission from this new state generates a photoluminescence peak that is red-shifted by as much as 254 meV from the nanotube's original excitonic transition. We also found that the attachment of electron-withdrawing substituents to carbon nanotubes systematically drives this defect state further down the energy ladder. Our experiments show that the material's photoluminescence quantum yield increases exponentially as a function of the shifted emission energy. This work lays the foundation for chemical control of defect quantum states in low-dimensional carbon materials.
[show abstract][hide abstract] ABSTRACT: We report femtosecond stimulated Raman spectroscopy measurements of lattice dynamics in semiconductor nanocrystals and characterize longitudinal optical (LO) phonon production during confinement-enhanced, ultrafast intraband relaxation. Stimulated Raman signals from unexcited CdSe nanocrystals produce a spectral shape similar to spontaneous Raman signals. Upon photoexcitation, stimulated Raman amplitude decreases owing to experimentally resolved ultrafast phonon generation rates within the lattice. We find a ∼600 fs, particle-size-independent depletion time attributed to hole cooling, evidence of LO-to-acoustic down-conversion, and LO phonon mode softening.
[show abstract][hide abstract] ABSTRACT: The influence of amino acid sequence on the secondary structure of peptide amphiphile (PAs) cylindrical micelles and fibers that are self-assembled in solution is studied using molecular dynamics simulations. Simulations for two choices of PAs were performed, starting with structures that have the correct overall shape, but which restructure considerably during the simulation, with one fiber being composed of valine rich PAs and the other of alanine rich PAs. Self-assembly is similar in both simulations, with stable fibers (diameter is 7.7–8 nm) obtained after 40 ns. We find that the valine rich PA fiber has a higher β-sheet population than the alanine rich fiber, and that the number of hydrogen bonds is higher. This behavior of the valine rich fiber is consistent with experimental measurements of higher stiffness, and it shows that stiffness can be varied while still maintaining self-assembly.
Journal of Nanoparticle Research 08/2013; 14(8). · 2.18 Impact Factor
[show abstract][hide abstract] ABSTRACT: The design and assembly of mechanically interlocked molecules, such as catenanes and rotaxanes, are dictated by various types of noncovalent interactions. In particular, [C-H···O] hydrogen-bonding and π-π stacking interactions in these supramolecular complexes have been identified as important noncovalent interactions. With this in mind, we examined the catenane 2·4PF6 using molecular mechanics (MM3), ab initio methods (HF, MP2), several versions of density functional theory (DFT) (B3LYP, M0X), and the dispersion-corrected method DFT-D3. Symmetry adapted perturbation theory (DFT-SAPT) provides the highest level of theory considered, and we use the DFT-SAPT results both to calibrate the other electronic structure methods, and the empirical potential MM3 force field that is often used to describe larger catenane and rotaxane structures where [C-H···O] hydrogen-bonding and π-π stacking interactions play a role. Our results indicate that the MM3 calculated complexation energies agree qualitatively with the energetic ordering from DFT-SAPT calculations with an aug-cc-pVTZ basis, both for structures dominated by [C-H···O] hydrogen-bonding and π-π stacking interactions. When the DFT-SAPT energies are decomposed into components, we find that electrostatic interactions dominate the [C-H···O] hydrogen-bonding interactions, while dispersion makes a significant contribution to π-π stacking. Another important conclusion is that DFT-D3 based on M06 or M06-2X provides interaction energies that are in near-quantitative agreement with DFT-SAPT. DFT results without the D3 correction have important differences compared to DFT-SAPT, while HF and even MP2 results are in poor agreement with DFT-SAPT.
The Journal of Physical Chemistry A 08/2013; · 2.77 Impact Factor
[show abstract][hide abstract] ABSTRACT: By combining targeted molecular dynamics (TMD) simulations, umbrella sampling, and the weighted histogram analysis method (WHAM), we have calculated the potential of mean force (PMF) for the transition between the bound and free states of peptide amphiphiles (PAs) in aqueous solution, with the bound state corresponding to a cylindrical micelle fiber. We specifically consider a collective reaction coordinate, the radius of gyration of the PAs, to describe assembly in this work. It is found that the free energy, enthalpy, and entropy differences between the free and bound states are -126 kcal/mol, -185 kcal/mol, and -190 cal/mol K, respectively, for the self-assembly process. This indicates that the driving force to form the micelle structure is enthalpic. The enthalpic driving forces originate from several factors, including the conformational energy of PAs, the electrostatic and van der Waals interaction energy between solvent molecules, and between solvent and PAs. Among these interactions, the solvent electrostatic interaction is the dominating one, contributing 54% of the total driving force. The PMF profile can be recognized as involving two stages of assembly: (1) PAs initially approach each other in mostly random configurations and loosely aggregate, resulting in significant desolvation and initiation of head-tail conformational reorganization; (2) PAs undergo a conformational disorder-to-order transition, including forming secondary structures that include more beta sheets and fewer random coils, along with tail-head core-shell alignment and condensation that leads to total exclusion of water from the core. The PMF decreases slowly in the first stage, but rapidly in the second. This study demonstrates a hierarchy of assembly steps in which PA structural changes, solvation and re-distribution of solvent molecules play significant roles in the PA self-assembly process.
The Journal of Physical Chemistry B 07/2013; · 3.61 Impact Factor
[show abstract][hide abstract] ABSTRACT: The ability to control pre-mRNA splicing with small molecules could facilitate the development of therapeutics or cell-based circuits that control gene function. Myotonic dystrophy type 1 is caused by the dysregulation of alternative pre-mRNA splicing due to sequestration of muscleblind-like 1 protein (MBNL1) by expanded, non-coding r(CUG) repeats (r(CUG)(exp)). Here we report two small molecules that induce or ameliorate alternative splicing dysregulation. A thiophene-containing small molecule (1) inhibits the interaction of MBNL1 with its natural pre-mRNA substrates. Compound (2), a substituted naphthyridine, binds r(CUG)(exp) and displaces MBNL1. Structural models show that 1 binds MBNL1 in the Zn-finger domain and that 2 interacts with UU loops in r(CUG)(exp). This study provides a structural framework for small molecules that target MBNL1 by mimicking r(CUG)(exp) and shows that targeting MBNL1 causes dysregulation of alternative splicing, suggesting that MBNL1 is thus not a suitable therapeutic target for the treatment of myotonic dystrophy type 1.
[show abstract][hide abstract] ABSTRACT: The chemical variety present in the organic electronics literature has motivated us to investigate potential nonbonding interactions often incorporated into conformational "locking" schemes. We examine a variety of potential interactions, including oxygen-sulfur, nitrogen-sulfur, and fluorine-sulfur, using accurate quantum-chemical wave function methods and Noncovalent Interaction (NCI) analysis on a selection of high-performing conjugated polymers and small molecules found in the literature. In addition, we evaluate a set of nonbonding interactions occurring between various heterocyclic and pendant atoms taken from a group of representative pi-conjugated molecules. Together with our survey and set of interactions, it is determined that while many nonbonding interactions possess weak binding capabilities, nontraditional hydrogen bonding interactions, namely oxygen-hydrogen (CH⋯O) and nitrogen-hydrogen (CH⋯N), are alone in inducing conformational control and enhanced planarity along a polymer or small molecule backbone at room temperature.
Journal of the American Chemical Society 06/2013; · 10.68 Impact Factor
[show abstract][hide abstract] ABSTRACT: We utilize a peptide-based methodology to prepare a diverse collection of double-helical gold nanoparticle superstructures having controllable handedness and structural metrics. These materials exhibit well-defined circular dichroism (CD) signatures at visible wavelengths owing to the collective dipole-dipole interactions between the nanoparticles. We couple theory and experiment to show how tuning the metrics and structure of the helices results in predictable and tailorable chirooptical properties. Finally, we experimentally and theoretically demonstrate that the intensity, position, and nature of the chirooptical activity can be carefully adjusted via silver overgrowth. These studies illustrate the utility of peptide-based nanoparticle assembly platforms for designing and preparing complex plasmonic materials with tailorable optical properties.
[show abstract][hide abstract] ABSTRACT: Periodic dielectric structures are typically integrated with a planar waveguide to create photonic band-edge modes for feedback in one-dimensional distributed feedback lasers and two-dimensional photonic-crystal lasers. Although photonic band-edge lasers are widely used in optics and biological applications, drawbacks include low modulation speeds and diffraction-limited mode confinement. In contrast, plasmonic nanolasers can support ultrafast dynamics and ultrasmall mode volumes. However, because of the large momentum mismatch between their nanolocalized lasing fields and free-space light, they suffer from large radiative losses and lack beam directionality. Here, we report lasing action from band-edge lattice plasmons in arrays of plasmonic nanocavities in a homogeneous dielectric environment. We find that optically pumped, two-dimensional arrays of plasmonic Au or Ag nanoparticles surrounded by an organic gain medium show directional beam emission (divergence angle <1.5° and linewidth <1.3 nm) characteristic of lasing action in the far-field, and behave as arrays of nanoscale light sources in the near-field. Using a semi-quantum electromagnetic approach to simulate the active optical responses, we show that lasing is achieved through stimulated energy transfer from the gain to the band-edge lattice plasmons in the deep subwavelength vicinity of the individual nanoparticles. Using femtosecond-transient absorption spectroscopy, we verified that lattice plasmons in plasmonic nanoparticle arrays could reach a 200-fold enhancement of the spontaneous emission rate of the dye because of their large local density of optical states.
[show abstract][hide abstract] ABSTRACT: Using on-wire lithography, we studied the emission properties of nanostructures made of a polythiophene disk separated by fixed nanoscopic distances from a plasmonic gold nanorod. The intense plasmonic field generated by the nanorod modifies the shape of the polythiophene emission spectrum, and the strong distance dependence of this modulation forms the basis for a new type of "plasmophore ruler". Simulations using the discrete dipole approximation (DDA) quantitatively support our experimental results. Importantly, this plasmophore ruler is independent of signal intensity and is effective up to 100 nm, which is more than two times larger than any reported value for rulers based on photoluminescence processes.
[show abstract][hide abstract] ABSTRACT: Steered molecular dynamics (SMD) simulations were applied to determine the potential of mean force for the self-assembly of peptide amphiphile (PA) nanofibers, specifically considering a single PA adding to a growing cylindrical nanofiber at 310 K. It is found that the free energy, enthalpy, and entropy differences for this assembly process are -67 kcal/mol, -71.5 kcal/ml, and -14.5 cal/mol K, respectively, and therefore that enthalpy provides the driving force for self-assembly to form a fiber. A pair-wise interaction analysis shows that both electrostatic and van der Waals interactions play important roles in the self-assembly process, with the van der Waals interaction being the larger effect. The mechanistic picture that emerges from this work is that as the PA is pulled from the fiber, the interaction evolves through three stages: (1) initially electrostatic interactions between the charged head of the pulled PA and other PAs, and between the pulled PA and solvent are dominant, (2) after the charged head emerges, the rest of the peptide comes out, with both PA-solvent electrostatic interactions and van der Waals interactions being significant, and (3) in the last step the alkane tail emerges, dominated by van der Waals interactions with either peptide or solvent.
The Journal of Physical Chemistry A 03/2013; · 2.77 Impact Factor
[show abstract][hide abstract] ABSTRACT: One class of functionally important RNA is repeating transcripts that cause disease through various mechanisms. For example, expanded CAG repeats can cause Huntington's and other disease through translation of toxic proteins. Herein, a crystal structure of r[5'UUGGGC(CAG)GUCC], a model of CAG expanded transcripts, refined to 1.65 Å resolution is disclosed that shows both anti-anti and syn-anti orientations for 1 × 1 nucleotide AA internal loops. Molecular dynamics (MD) simulations using AMBER force field in explicit solvent were run for over 500 ns on the model systems r(5'GCGCAGCGC) (MS1) and r(5'CCGCAGCGG) (MS2). In these MD simulations, both anti-anti and syn-anti AA base pairs appear to be stable. While anti-anti AA base pairs were dynamic and sampled multiple anti-anti conformations, no syn-anti ↔ anti-anti transformations were observed. Umbrella sampling simulations were run on MS2, and a 2D free energy surface was created to extract transformation pathways. In addition, an explicit solvent MD simulation over 800 ns was run on r[5'GGGC(CAG)GUCC], which closely represents the refined crystal structure. One of the terminal AA base pairs (syn-anti conformation), transformed to anti-anti conformation. The pathway followed in this transformation was the one predicted by umbrella sampling simulations. Further analysis showed a binding pocket near AA base pairs in syn-anti conformations. Computational results combined with the refined crystal structure show that global minimum conformation of 1 × 1 nucleotide AA internal loops in r(CAG) repeats is anti-anti but can adopt syn-anti depending on the environment. These results are important to understand RNA dynamic-function relationships and to develop small molecules that target RNA dynamic ensembles.
Journal of the American Chemical Society 03/2013; 135(9):3528-38. · 10.68 Impact Factor
[show abstract][hide abstract] ABSTRACT: Multivalent nanostructures are an increasingly important player in the
self-assembly of optically responsive superlattices. Understanding the
role nanostructure coordination plays in the ordering of superlattice
assemblies is crucial for the plasmonic response of the material. We
developed a simple design rule for the assembly of multivalent DNA-Au
triangular nanoprisms into 1D ordered superlattices based on both the
length of the valent DNA and the size of the prism. Using MD
simulations, we describe an order parameter that captures the
short-range order of the mesoscale assembly controlled by the design
rule. The order parameter shows that even short chains of prisms have a
high-degree of orientational order when 1D superlattices are formed.
Unlike isotropic polyvalent nanostructures, we find the highly oriented
prism superlattices lose orientational order in a multistage fashion
through loss of coordination during melting.
[show abstract][hide abstract] ABSTRACT: This paper describes measurements of the dynamics of hot electron cooling in photoexcited gold nanoparticles (Au NPs) with diameters of ∼3.5 nm, and passivated with either a hexadecylamine or hexadecanethiolate adlayer, using ultrafast transient absorption spectroscopy. Fits of these dynamics with temperature-dependent Mie theory reveal that both the electronic heat capacity and the electron-phonon coupling constant are larger for the thiolated NPs than for the aminated NPs, by 40% and 30%, respectively. Density functional theory calculations on ligand-functionalized Au slabs show that the increase in these quantities is due to an increased electronic density of states near the Fermi level upon ligand exchange from amines to thiolates. The lifetime of hot electrons, which have thermalized from the initial plasmon excitation, increases with increasing electronic heat capacity, but decreases with increasing electron-phonon coupling, so the effects of changing surface chemistry on these two quantities partially cancel to yield a hot electron lifetime of thiolated NPs that is only 20% longer than that of aminated NPs. This analysis also reveals that incorporation of a temperature-dependent electron-phonon coupling constant is necessary to adequately fit the dynamics of electron cooling.
Proceedings of the National Academy of Sciences 02/2013; · 9.74 Impact Factor