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1.  Electronic and transport properties of kinked graphene 
Summary
Local curvature, or bending, of a graphene sheet is known to increase the chemical reactivity presenting an opportunity for templated chemical functionalisation. Using first-principles calculations based on density functional theory (DFT), we investigate the reaction barrier reduction for the adsorption of atomic hydrogen at linear bends in graphene. We find a significant barrier lowering (≈15%) for realistic radii of curvature (≈20 Å) and that adsorption along the linear bend leads to a stable linear kink. We compute the electronic transport properties of individual and multiple kink lines, and demonstrate how these act as efficient barriers for electron transport. In particular, two parallel kink lines form a graphene pseudo-nanoribbon structure with a semimetallic/semiconducting electronic structure closely related to the corresponding isolated ribbons; the ribbon band gap translates into a transport gap for electronic transport across the kink lines. We finally consider pseudo-ribbon-based heterostructures and propose that such structures present a novel approach for band gap engineering in nanostructured graphene.
doi:10.3762/bjnano.4.12
PMCID: PMC3596121  PMID: 23503656
adsorption and reactivity; curvature effects; DFT calculations; electronic transport; graphene nanoribbons; graphene nanostructuring
2.  Size-dependent phase diagrams of metallic alloys: A Monte Carlo simulation study on order–disorder transitions in Pt–Rh nanoparticles 
Summary
Nanoparticles of Pt–Rh were studied by means of lattice-based Monte Carlo simulations with respect to the stability of ordered D022- and 40-phases as a function of particle size and composition. By thermodynamic integration in the semi-grand canonical ensemble, phase diagrams for particles with a diameter of 7.8 nm, 4.3 nm and 3.1 nm were obtained. Size-dependent trends such as the lowering of the critical ordering temperature, the broadening of the compositional stability range of the ordered phases, and the narrowing of the two-phase regions were observed and discussed in the context of complete size-dependent nanoparticle phase diagrams. In addition, an ordered surface phase emerges at low temperatures and low platinum concentration. A decrease of platinum surface segregation with increasing global platinum concentration was observed, when a second, ordered phase is formed inside the core of the particle. The order–disorder transitions were analyzed in terms of the Warren–Cowley short-range order parameters. Concentration-averaged short-range order parameters were used to remove the surface segregation bias of the conventional short-range order parameters. Using this procedure, it was shown that the short-range order in the particles at high temperatures is bulk-like.
doi:10.3762/bjnano.3.1
PMCID: PMC3304325  PMID: 22428091
Monte Carlo simulation; nanoparticles; nanothermodynamics; phase diagram; Pt-Rh; thermodynamics
3.  Surface induced self-organization of comb-like macromolecules 
Summary
We present a review of the theoretical and experimental evidence for the peculiar properties of comb copolymers, demonstrating the uniqueness of these materials among other polymer architectures. These special properties include an increase in stiffness upon increasing side-chain length, the spontaneous curvature of adsorbed combs, rod–globule transition, and specific intramolecular self-assembly. We also propose a theory of chemically heterogeneous surface nanopattern formation in ultrathin films of comblike macromolecules containing two different types (A and B) of incompatible side chains (so-called binary combs). Side chains of the binary combs are strongly adsorbed on a surface and segregated with respect to the backbone. The thickness of surface domains formed by the B side chains is controlled by the interaction with the substrate. We predict the stability of direct and inverse disc-, torus- and stripelike nanostructures. Phase diagrams of the film are constructed.
doi:10.3762/bjnano.2.61
PMCID: PMC3190627  PMID: 22003463
comb copolymers; macromolecules; adsorption; self-organization
4.  Plasmonic nanostructures fabricated using nanosphere-lithography, soft-lithography and plasma etching 
Summary
We present two routes for the fabrication of plasmonic structures based on nanosphere lithography templates. One route makes use of soft-lithography to obtain arrays of epoxy resin hemispheres, which, in a second step, can be coated by metal films. The second uses the hexagonal array of triangular structures, obtained by evaporation of a metal film on top of colloidal crystals, as a mask for reactive ion etching (RIE) of the substrate. In this way, the triangular patterns of the mask are transferred to the substrate through etched triangular pillars. Making an epoxy resin cast of the pillars, coated with metal films, allows us to invert the structure and obtain arrays of triangular holes within the metal. Both fabrication methods illustrate the preparation of large arrays of nanocavities within metal films at low cost.
Gold films of different thicknesses were evaporated on top of hemispherical structures of epoxy resin with different radii, and the reflectance and transmittance were measured for optical wavelengths. Experimental results show that the reflectivity of coated hemispheres is lower than that of coated polystyrene spheres of the same size, for certain wavelength bands. The spectral position of these bands correlates with the size of the hemispheres. In contrast, etched structures on quartz coated with gold films exhibit low reflectance and transmittance values for all wavelengths measured. Low transmittance and reflectance indicate high absorbance, which can be utilized in experiments requiring light confinement.
doi:10.3762/bjnano.2.49
PMCID: PMC3190615  PMID: 22003451
nanosphere-lithography; near-field enhancement; plasma etching; soft-lithography; surface plasmons
5.  Towards a scalable and accurate quantum approach for describing vibrations of molecule–metal interfaces 
Summary
We present a theoretical framework for the computation of anharmonic vibrational frequencies for large systems, with a particular focus on determining adsorbate frequencies from first principles. We give a detailed account of our local implementation of the vibrational self-consistent field approach and its correlation corrections. We show that our approach is both robust, accurate and can be easily deployed on computational grids in order to provide an efficient computational tool. We also present results on the vibrational spectrum of hydrogen fluoride on pyrene, on the thiophene molecule in the gas phase, and on small neutral gold clusters.
doi:10.3762/bjnano.2.48
PMCID: PMC3190614  PMID: 22003450
computational scaling; grid computing; molecule–metal interactions; periodic density functional theory; vibrational theory
6.  Charge transfer through single molecule contacts: How reliable are rate descriptions? 
Summary
Background: The trend for the fabrication of electrical circuits with nanoscale dimensions has led to impressive progress in the field of molecular electronics in the last decade. However, a theoretical description of molecular contacts as the building blocks of future devices is challenging, as it has to combine the properties of Fermi liquids in the leads with charge and phonon degrees of freedom on the molecule. Outside of ab initio schemes for specific set-ups, generic models reveal the characteristics of transport processes. Particularly appealing are descriptions based on transfer rates successfully used in other contexts such as mesoscopic physics and intramolecular electron transfer. However, a detailed analysis of this scheme in comparison with numerically exact solutions is still elusive.
Results: We show that a formulation in terms of transfer rates provides a quantitatively accurate description even in domains of parameter space where strictly it is expected to fail, e.g., at lower temperatures. Typically, intramolecular phonons are distributed according to a voltage driven steady state that can only roughly be captured by a thermal distribution with an effective elevated temperature (heating). An extension of a master equation for the charge–phonon complex, to effectively include the impact of off-diagonal elements of the reduced density matrix, provides very accurate solutions even for stronger electron–phonon coupling.
Conclusion: Rate descriptions and master equations offer a versatile model to describe and understand charge transfer processes through molecular junctions. Such methods are computationally orders of magnitude less expensive than elaborate numerical simulations that, however, provide exact solutions as benchmarks. Adjustable parameters obtained, e.g., from ab initio calculations allow for the treatment of various realizations. Even though not as rigorously formulated as, e.g., nonequilibrium Green’s function methods, they are conceptually simpler, more flexible for extensions, and from a practical point of view provide accurate results as long as strong quantum correlations do not modify the properties of the relevant subunits substantially.
doi:10.3762/bjnano.2.47
PMCID: PMC3190613  PMID: 22003449
inelastic charge transfer; molecular contacts; nonequilibrium distributions; numerical simulations; rate equations
7.  Simulation of bonding effects in HRTEM images of light element materials 
Summary
The accuracy of multislice high-resolution transmission electron microscopy (HRTEM) simulation can be improved by calculating the scattering potential using density functional theory (DFT) [1–2]. This approach accounts for the fact that electrons in the specimen are redistributed according to their local chemical environment. This influences the scattering process and alters the absolute and relative contrast in the final image. For light element materials with well defined geometry, such as graphene and hexagonal boron nitride monolayers, the DFT based simulation scheme turned out to be necessary to prevent misinterpretation of weak signals, such as the identification of nitrogen substitutions in a graphene network. Furthermore, this implies that the HRTEM image does not only contain structural information (atom positions and atomic numbers). Instead, information on the electron charge distribution can be gained in addition.
In order to produce meaningful results, the new input parameters need to be chosen carefully. Here we present details of the simulation process and discuss the influence of the main parameters on the final result. Furthermore we apply the simulation scheme to three model systems: A single atom boron and a single atom oxygen substitution in graphene and an oxygen adatom on graphene.
doi:10.3762/bjnano.2.45
PMCID: PMC3190611  PMID: 22003447
chemical bonding; DFT; graphene; HRTEM
8.  Influence of water on the properties of an Au/Mpy/Pd metal/molecule/metal junction 
Summary
The geometric and electronic structure of the metal–molecule interface in metal/molecule/metal junctions is of great interest since it affects the functionality of such units in possible nanoelectronic devices. We have investigated the interaction between water and a palladium monolayer of a Au(111)/4-mercaptopyridine/Pd junction by means of DFT calculations. A relatively strong bond between water and the palladium monolayer of the Au/Mpy/Pd complex is observed via a one-fold bond between the oxygen atom of the water molecule and a Pd atom. An isolated H2O molecule adsorbs preferentially in a flat-lying geometry on top of a palladium atom that is at the same time also bound to the nitrogen atom of a Mpy molecule of the underlying self-assembled monolayer. The electronic structure of these Pd atoms is considerably modified which is reflected in a reduced local density of states at the Fermi energy. At higher coverages, water can be arranged in a hexagonal ice-like bilayer structure in analogy to water on bulk metal surfaces, but with a much stronger binding which is dominated by O–Pd bonds.
doi:10.3762/bjnano.2.44
PMCID: PMC3190610  PMID: 22003446
density functional calculations; self-assembled monolayers; water adsorption

Results 1-8 (8)