Evolution of hexagonal patterns from controlled initial conditions in a Bénard-Marangoni convection experiment

We report quantitative measurements of both wave number selection and defect motion in nonequilibrium hexagonal patterns. A novel optical technique ("thermal laser writing") is used to imprint initial patterns with selected characteristics in a Bénard-Marangoni convection experiment. Initial patterns of ideal hexagons are imposed to determine the band of stable pattern wave numbers while initial patterns containing an isolated penta-hepta defect are imprinted to study defect propagation directions and velocities. The experimental results are compared to recent theoretical predictions.     

Steered molecular dynamics studies of the potential of mean force of a Na+ or K+ ion in a cyclic peptide nanotube

Potential of mean force (PMF) profiles of a single Na+ or K+ ion passing through a cyclic peptide nanotube, cyclo[-(D-Ala-Glu-D-Ala-Gln)2-], in water are calculated to provide insight into ion transport and to understand the conductance difference between these two ions. The PMF profiles are obtained by performing steered molecular dynamics (SMD) simulations that are based on the Jarzynski equality. The computed PMF profiles for both ions show barriers of around 2.4 kcal/mol at the channel entrances and exits and energy wells in the middle of the tube. The energy barriers, so-called dielectric energy barriers, arise due to the desolvation of water molecules when ions move across the nanotube, and the energy wells appear as a result of attractive interactions between the cations and negatively charged carbonyl oxygens on the backbone of the tube. We find more and deeper energy wells in the PMF profile for Na+ than for K+, which suggests that Na+ ions have a longer residence time inside the nanotube and that permeation of Na+ ions is reduced compared to K+ ions. Calculations of the radial distribution functions (RDF) between the ions and oxygens in the water molecules and in carbonyl groups on the tube and an investigation of the orientations of the carbonyl groups show that, in contrast with the dynamic carbonyl groups observed in the selectivity filter of the KcsA ion channel, the carbonyl groups in the cyclic peptide nanotube are relatively rigid, with only slight reorientation of the carbonyl groups as the cations pass through. The rigidity of the carbonyl groups in the cyclic peptide nanotube can be attributed to their role in hydrogen bonding, which is responsible for the tube structure. Comparison of the PMF profiles with the electrostatic energy profiles calculated from the Poisson-Boltzmann (PB) equation, a dielectric continuum model, reveals that the dielectric continuum model breaks down in the confined region within the tube that governs ion transport.     

A coupled states quantum reactive scattering study of H + D2 → HD + D ATErel(υ = j = 0) = 0.55 eV

In this paper we present the results of accurate quantum coupled states calculations for the H + D₂ → HD + D reaction at 0.55 eV translational energy (relative to υ = 0, j = 0) using the accurate LSTH potential surface.     

A DFT study of the ground state multiplicities of linear vs angular polyheteroacenes

Unrestricted density functional calculations in combination with the broken-symmetry approach and spin-projection methods have been employed to study a series of formally 4n pi antiaromatic linear and angular polyheteroacenes. Calculations show that the linear polyheteroacene molecules have either stable singlet zwitterionic 6-9 or singlet diradical 5 ground states because they sacrifice the aromaticity of the central arene to form two independent cyanines. The corresponding angular compounds 10-14 have robust triplet states, since they cannot create independent cyanines to escape their overall antiaromaticity. An analysis based on the SOMO-SOMO energy splittings, their spatial distributions, and the spin density populations for the triplet states is presented to clarify the factors that determine their ground state multiplicities.     

Theoretical investigation of hyperthermal reactions at the gas-liquid interface: O (3P) and squalane

Hyperthermal collisions (5 eV) of ground-state atomic oxygen [O ((3)P)] with a liquid-saturated hydrocarbon, squalane (C(30)H(62)), have been studied using QM/MM hybrid "on-the-fly" direct dynamics. The surface structure of the liquid squalane is obtained from a classical molecular dynamics simulation using the OPLS-AA force field. The MSINDO semiempirical Hamiltonian is combined with OPLS-AA for the QM/MM calculations. In order to achieve a more consistent and efficient simulation of the collisions, we implemented a dynamic partitioning of the QM and MM atoms in which atoms are assigned to QM or MM regions based on their proximity to "seed" (open-shell) atoms that determine where bond making/breaking can occur. In addition, the number of seed atoms is allowed to increase or decrease as time evolves so that multiple reactive events can be described. The results show that H abstraction is the most important process for all incident angles, with H elimination, double H abstraction, and C-C bond cleavage also being important. A number of properties of these reactive channels, as well as inelastic nonreactive scattering, are investigated, including angular and translational energy distributions, the effect of incident collision angle, variation with depth of the reactive event within the liquid, with the reaction site on the hydrocarbon, and the effect of dynamics before and after reaction (direct reaction versus trapping reaction-desorption).     

Observation of a quadrupole plasmon mode for a colloidal solution of gold nanoprisms

The synthesis and optical properties of single crystalline gold nanoprisms have been investigated. A three-step mediated seed growth process in an aqueous solution generated gold nanoprisms with a relatively homogeneous size distribution. The purity of these nanostructures has allowed us to observe a weak quadrupole resonance in addition to a strong dipole resonance associated with these novel structures. The experimental optical spectra agree with discrete dipole approximation calculations that have been modeled from the dimensions of gold nanoprisms produced in this synthesis.     

Significant nonadiabatic effects in the S(1D) + HD reaction

A nonadiabatic quantum dynamics calculation involving four coupled potential energy surfaces (two degenerate 3A' ', one 3A', and one 1A') and the spin-orbit coupling matrix for these states is reported for the title reaction. The results show that the important discrepancy between theoretically calculated and experimentally measured intramolecular isotope effects can at least in part be attributed to significant nonadiabatic effects.     

What controls the melting properties of DNA-linked gold nanoparticle assemblies?

We report a series of experiments and a theoretical model designed to systematically define and evaluate the relative importance of nanoparticle, oligonucleotide, and environmental variables that contribute to the observed sharp melting transitions associated with DNA-linked nanoparticle structures. These variables include the size of the nanoparticles, the surface density of the oligonucleotides on the nanoparticles, the dielectric constant of the surrounding medium, target concentration, and the position of the nanoparticles with respect to one another within the aggregate. The experimental data may be understood in terms of a thermodynamic model that attributes the sharp melting to a cooperative mechanism that results from two key factors: the presence of multiple DNA linkers between each pair of nanoparticles and a decrease in the melting temperature as DNA strands melt due to a concomitant reduction in local salt concentration. The cooperative melting effect, originating from short-range duplex-to-duplex interactions, is independent of DNA base sequences studied and should be universal for any type of nanostructured probe that is heavily functionalized with oligonucleotides. Understanding the fundamental origins of the melting properties of DNA-linked nanoparticle aggregates (or monolayers) is of paramount importance because these properties directly impact one's ability to formulate high sensitivity and selectivity DNA detection systems and construct materials from these novel nanoparticle materials.