Kohn-Sham Decomposition in Real-Time Time-Dependent Density-Functional Theory: An Efficient Tool for Analyzing Plasmonic Excitations.

Electronic excitations can be efficiently analyzed in terms of the underlying Kohn-Sham (KS) electron-hole transitions. While such a decomposition is readily available in the linear-response time-dependent density-functional theory (TDDFT) approaches based on the Casida equations, a comparable analysis is less commonly conducted within the real-time-propagation TDDFT (RT-TDDFT). To improve this situation, we present here an implementation of a KS decomposition tool within the local-basis-set RT-TDDFT code in the free GPAW package. Our implementation is based on postprocessing of data that is readily available during time propagation, which is important for retaining the efficiency of the underlying RT-TDDFT to large systems. After benchmarking our implementation on small benzene derivatives by explicitly reconstructing the Casida eigenvectors from RT-TDDFT, we demonstrate the performance of the method by analyzing the plasmon resonances of icosahedral silver nanoparticles up to Ag561. The method provides a clear description of the splitting of the plasmon in small nanoparticles due to individual single-electron transitions as well as the formation of a distinct d-electron-screened plasmon resonance in larger nanoparticles.

Computational model for noncontact atomic force microscopy: energy dissipation of cantilever.

We propose a computational model for noncontact atomic force microscopy (AFM) in which the atomic force between the cantilever tip and the surface is calculated using a molecular dynamics method, and the macroscopic motion of the cantilever is modeled by an oscillating spring. The movement of atoms in the tip and surface is connected with the oscillating spring using a recently developed coupling method. In this computational model, the oscillation energy is dissipated, as observed in AFM experiments. We attribute this dissipation to the hysteresis and nonconservative properties of the interatomic force that acts between the atoms in the tip and sample surface. The dissipation rate strongly depends on the parameters used in the computational model.

Quantized Evolution of the Plasmonic Response in a Stretched Nanorod.

Quantum aspects, such as electron tunneling between closely separated metallic nanoparticles, are crucial for understanding the plasmonic response of nanoscale systems. We explore quantum effects on the response of the conductively coupled metallic nanoparticle dimer. This is realized by stretching a nanorod, which leads to the formation of a narrowing atomic contact between the two nanorod ends. Based on first-principles time-dependent density-functional-theory calculations, we find a discontinuous evolution of the plasmonic response as the nanorod is stretched. This is especially pronounced for the intensity of the main charge-transfer plasmon mode. We show the correlation between the observed discontinuities and the discrete nature of the conduction channels supported by the formed atomic-sized junction.

Nanoplasmonics simulations at the basis set limit through completeness-optimized, local numerical basis sets.

We present an approach for generating local numerical basis sets of improving accuracy for first-principles nanoplasmonics simulations within time-dependent density functional theory. The method is demonstrated for copper, silver, and gold nanoparticles that are of experimental interest but computationally demanding due to the semi-core d-electrons that affect their plasmonic response. The basis sets are constructed by augmenting numerical atomic orbital basis sets by truncated Gaussian-type orbitals generated by the completeness-optimization scheme, which is applied to the photoabsorption spectra of homoatomic metal atom dimers. We obtain basis sets of improving accuracy up to the complete basis set limit and demonstrate that the performance of the basis sets transfers to simulations of larger nanoparticles and nanoalloys as well as to calculations with various exchange-correlation functionals. This work promotes the use of the local basis set approach of controllable accuracy in first-principles nanoplasmonics simulations and beyond.

Dynamical coupling of plasmons and molecular excitations by hybrid quantum/classical calculations: time-domain approach.

The presence of plasmonic material influences the optical properties of nearby molecules in untrivial ways due to the dynamical plasmon-molecule coupling. We combine quantum and classical calculation schemes to study this phenomenon in a hybrid system that consists of a Na(2) molecule located in the gap between two Au/Ag nanoparticles. The molecule is treated quantum-mechanically with time-dependent density-functional theory, and the nanoparticles with quasistatic classical electrodynamics. The nanoparticle dimer has a plasmon resonance in the visible part of the electromagnetic spectrum, and the Na(2) molecule has an electron-hole excitation in the same energy range. Due to the dynamical interaction of the two subsystems the plasmon and the molecular excitations couple, creating a hybridized molecular-plasmon excited state. This state has unique properties that yield e.g. enhanced photoabsorption compared to the freestanding Na(2) molecule. The computational approach used enables decoupling of the mutual plasmon-molecule interaction, and our analysis verifies that it is not legitimate to neglect the back coupling effect when describing the dynamical interaction between plasmonic material and nearby molecules. Time-resolved analysis shows nearly instantaneous formation of the coupled state, and provides an intuitive picture of the underlying physics.

Coronene encapsulation in single-walled carbon nanotubes: stacked columns, peapods, and nanoribbons.

Encapsulation of coronene inside single-walled carbon nanotubes (SWNTs) was studied under various conditions. Under high vacuum, two main types of molecular encapsulation were observed by using transmission electron microscopy: coronene dimers and molecular stacking columns perpendicular or tilted (45-60°) with regard to the axis of the SWNTs. A relatively small number of short nanoribbons or polymerized coronene molecular chains were observed. However, experiments performed under an argon atmosphere (0.17 MPa) revealed reactions between the coronene molecules and the formation of hydrogen-terminated graphene nanoribbons. It was also observed that the morphology of the encapsulated products depend on the diameter of the SWNTs. The experimental results are explained by using density functional theory calculations through the energies of the coronene molecules inside the SWNTs, which depend on the orientation of the molecules and the diameter of the tubes.

Fast convergence to equilibrium for long-chain polymer melts using a MD/continuum hybrid method.

Effective and fast convergence toward an equilibrium state for long-chain polymer melts is realized by a hybrid method coupling molecular dynamics and the elastic continuum. The required simulation time to achieve the equilibrium state is reduced compared with conventional equilibration methods. The polymers move on a wide range phase space due to large-scale fluctuation generated by the elastic continuum. A variety of chain structures is generated in the polymer melt which results in the fast convergence to the equilibrium state.

Synthesis of graphene nanoribbons encapsulated in single-walled carbon nanotubes.

A novel material, graphene nanoribbons encapsulated in single-walled carbon nanotubes (GNR@SWNT), was synthesized using confined polymerization and fusion of polycyclic aromatic hydrocarbon (PAH) molecules. Formation of the GNR is possible due to confinement effects provided by the one-dimensional space inside nanotubes, which helps to align coronene or perylene molecules edge to edge to achieve dimerization and oligomerization of the molecules into long nanoribbons. Almost 100% filling of SWNT with GNR is achieved while nanoribbon length is limited only by the length of the encapsulating nanotube. The PAH fusion reaction provides a very simple and easily scalable method to synthesize GNR@SWNT in macroscopic amounts. First-principle simulations indicate that encapsulation of the GNRs is energetically favorable and that the electronic structure of the encapsulated GNRs is the same as for the free-standing ones, pointing to possible applications of the GNR@SWNT structures in photonics and nanoelectronics.

Mechanisms of postsynthesis doping of boron nitride nanostructures with carbon from first-principles simulations.

Electron-beam-mediated postsynthesis doping of boron-nitride nanostructures with carbon atoms [Nature (London) 464, 571 (2010); J. Am. Chem. Soc. 132, 13 692 (2010)] was recently demonstrated, thus opening a new way to control the electronic properties of these systems. Using density-functional theory static and dynamic calculations, we show that the substitution process is governed not only by the response of such systems to irradiation, but also by the energetics of the atomic configurations, especially when the system is electrically charged. We suggest using spatially localized electron irradiation for making carbon islands and ribbons embedded into BN sheets. We further study the magnetic and electronic properties of such hybrid nanostructures and show that triangular carbon islands embedded into BN sheets possess magnetic moments, which can be switched on and off by electrically charging the structure.

Migration and localization of metal atoms on strained graphene.

Reconstructed point defects in graphene are created by electron irradiation and annealing. By applying electron microscopy and density functional theory, it is shown that the strain field around these defects reaches far into the unperturbed hexagonal network and that metal atoms have a high affinity to the nonperfect and strained regions of graphene. Metal atoms are attracted by reconstructed defects and bonded with energies of about 2 eV. The increased reactivity of the distorted π-electron system in strained graphene allows us to attach metal atoms and to tailor the properties of graphene.

Intrinsic n-type behavior in transparent conducting oxides: a comparative hybrid-functional study of In2O3, SnO2, and ZnO.

We present a comparative study of oxygen vacancies in In2O3, SnO2, and ZnO based on the hybrid-functional method within the density-functional theory (DFT). For In2O3 and SnO2, our results provide strong evidence of shallow donor states at oxygen vacancies. In comparison with the (semi)local exchange-correlation approximations in DFT, the hybrid-functional method strongly lowers the formation energy of the positive charge state and keeps that of the neutral state nearly intact. The trend is analyzed in terms of changes in lattice relaxation energies and in electron energy levels near the band gap. The existence of shallow donor states at oxygen vacancies and the consequent n-type conductivity are in line with experimental findings. The results invalidate some former theoretical interpretations based on standard DFT calculations.

Electronic energy band structure of the double perovskite Ba2MnWO6.

The electronic and magnetic structures of the double perovskite oxide Ba 2MnWO6 (BMW) were determined by employing the density functional theory within the generalized gradient approximation (GGA) + U approach. BMW is considered a prototype double perovskite due to its high degree of B-site ordering and is a good case study for making a comparison between computations and experiments. By adjusting the U-parameter, the electronic energy band structure and magnetic properties, which were consistent with the experimental results, were obtained. These computations revealed that the valence bands are mainly formed from Mn 3d and O 2p states, while the conduction bands are derived from W 5d and O 2p states. The localized bands composed from Mn 3d states are located in the bandgap. The results imply that the formation of polarons in the conduction band initiate the resonance Raman modes observed as a series of equidistant peaks.

Photoabsorption spectra of small fullerenes and Si-heterofullerenes.

We study the spectral properties of two kinds of derivatives of the carbon fullerene C(60), small fullerenes and Si-heterofullerenes, by ab initio calculations. The principal method of study is the time-dependent density-functional theory in its full time-propagation form. C(20), C(28), C(32), C(36), and C(50), the most stable small fullerenes in the range of C(20)-C(50), are found to have characteristic features in their optical absorption spectra, originating from the geometry of the molecules in question. The comparison of measured and calculated absorption spectra is found to be a useful tool in differentiating between different, almost isoenergetic ground state structure candidates of small fullerenes. Substitutionally doped fullerenes are of interest due to their enhanced chemical reactivity. It is suggested that the doping degree can be obtained by studying the absorption spectra. For example, it is observed that the spectra gradually change when doping C(60) up to C(48)Si(12) so that absorption in the visible and near infrared regions increases.

Photoabsorption in sodium clusters on the basis of time-dependent density-functional theory.

The photoabsorption spectra of a continuous series of Na(n) clusters (n

Photoabsorption spectra of boron nitride fullerenelike structures.

Optical absorption spectra have been calculated for a series of boron nitride fullerenelike cage structures BnNn of sizes n=12-36. The method used is a real-time, real-space implementation of the time-dependent density-functional theory, involving the full time propagation of the time-dependent Kohn-Sham equations. The spectra are found to be a possible tool for distinguishing between different boron nitride fullerene species and isomers. The trends and differences in the spectra are found to be related to the general geometry of the molecules. Comparison between local-density and generalized-gradient approximations for electron exchange-correlation functionals shows that both of them produce essentially the same spectral characteristics.

L-alanine in a droplet of water: a density-functional molecular dynamics study.

We report the results of a Born-Oppenheimer molecular dynamics study on an L-alanine amino acid in neutral aqueous solution. The whole system, the L-alanine zwitterion and 50 water molecules, was treated quantum mechanically. We found that the hydrophobic side chain (R = CH3) defines the trajectory path of the molecule. Initially fully hydrated in an isolated droplet of water, the amino acid moves to the droplet's surface, exposing its hydrophobic methyl group and alpha-hydrogen out of the water. The structure of an L-alanine with the methyl group exposed to the water surface was found to be energetically favorable compared to a fully hydrated molecule. The dynamic behavior of the system suggests that the first hydration shell of the amino acid is localized around carboxylate (CO2-) and ammonium (NH3+) functional groups; it is highly ordered and quite rigid. In contrast, the hydration shell around the side chain is much less structured, suggesting a modest influence of the methyl group on the structure of water. The number of water molecules in the first hydration shell of an alanine molecule is constantly changing; the average number was found to equal 7. The molecular dynamics results show that L-alanine in water does not have a preferred conformation, as all three of the molecule's functional sites (i.e., CH3, NH3+, CO2-) perform rotational movements around the C(alpha)-site bond.

Structure and dynamics of dioxygen bound to cobalt and iron heme.

In this study we use ab initio molecular dynamics simulations to analyze the structure and dynamics of the oxygen ligand in models of the oxymyoglobin active site and its cobalt-substituted analog. Our calculations are performed for iron-porphyrin and cobalt-porphyrin complexes with imidazole and oxygen as axial ligands, and we investigate the effect of the distal histidine in the structure and dynamics of the metal-oxygen unit (MeO(2), Me = Fe, Co). We find that the interaction between the distal histidine and the oxygen ligand is stronger for the cobalt complex than for the iron one, consistent with the superoxide ion character of the bound O(2). The dynamics of the O(2) ligand can be described as oscillations of the O-O axis projection on the porphyrin plane within a porphyrin quadrant combined with frequent jumps from one quadrant to another. However, the ligand motion is significantly faster for CoO(2) compared to FeO(2). As a result, the iron complex shows localized ligand sites, whereas for cobalt several configurations are possible. This gives support to the highly dynamic motion of the oxygen ligand found in several experiments on cobalt oxymyoglobin and model complexes and underlines the higher mobility of the CoO(2) fragment compared to FeO(2).

Measuring site-specific cluster-surface bond formation.

Recent advances in dynamic force microscopy show that it is possible to measure the forces between atomically sharp tips and particular atomic positions on surfaces as a function of distance. However, on most ionic surfaces, the positive and negative ions can so far not be distinguished. In this paper, we use the CaF2(111) surface, where atomic resolution force microscopy has allowed identification of the positions of the Ca2+ and F- ions in the obtained images, to demonstrate that short-range interaction forces can be measured selectively above chemically identified surface sites. Combining experimental and theoretical results allows a quantification of the strength and distance dependence of the interaction of a tip-terminating cluster with particular surface ions and reveals details of cluster and surface relaxation. Further development of this approach will provide new insight into mechanisms of chemical bond formation between clusters, cluster deposition at surfaces, processes in adhesion and tribology, and single atom manipulation with the force microscope.