Stability of Subnanometer MoS Wires under a Realistic Environment.

The interaction of small molecules with low-dimensional structures plays a major role in many important practical processes such as metal hydride formation, energy storage systems, and catalysis. In this work, we carried out first-principles density functional theory calculations of hydrogen and oxygen adsorption as well as their diffusion on subnanometer MoS nanowires. The nanowires are robust against adsorption of hydrogen. On the other hand, interaction with oxygen shows that the nanowires can oxidize with a small barrier (0.20 eV). In addition, our findings indicate that the interaction with hydrogen or oxygen does not modify the metallic character of the nanowire. The calculations also show that the singlet state is the most stable for 2O adsorbed on the MoS nanowire. Such results open the path for understanding the behavior of MoS nanowires under a realistic environment.

Electronic structure of molecular hydrogen in MoS2nanopores.

Atom controlled sub-nanometer MoS2pores have been recently fabricated with promising applications, such gas sensing, hydrogen storage and DNA translocation. In this work we carried out first-principles calculations of hydrogen adsorption in tiny MoS2nanopores. Some of the pores show metallic behaviour whereas others have a sizeable band gap. Whereas adsorption of molecular hydrogen on bare pores are dominated by physisorption, adsorption in the nanopores show chemisorption behaviour with high selectivity depending on the pore inner termination. Finally, we show that functionalization with copper atoms leads to does not improve dignificantly the adsorption energies of selected pores.

Oxygen vacancy diffusion in bare ZnO nanowires.

Oxygen vacancies (VO) are known to be common native defects in zinc oxide (ZnO) and to play important roles in many applications. Based on density functional theory, we present a study for the migration of oxygen vacancies in ultra-thin ZnO nanowires (NWs). We find that under equilibrium growth conditions VO has a higher formation energy (Ef) inside the wire than that at shallow sites and surface sites, with different geometric relaxations and structural reconstructions. The migration of VO has lower barriers in the NW than in the bulk and is found to be energetically favorable in the direction from the bulk to the surface. These results imply a higher concentration of VO at surface sites and also a relative ease of diffusion in the NW structure. Our results support the previous experimental observations and are important for the development of ZnO-based devices in photocatalysis and optoelectronics.

Formation of Helices in Graphene Nanoribbons under Torsion.

We use objective boundary conditions and self-consistent charge density-functional-based tight-binding to simulate at the atomistic scale the formation of helices in narrow graphene nanoribbons with armchair edges terminated with fluorine and hydrogen. We interpret the microscopic data using an inextensible, unshearable elastic rod model, which considers both bending and torsional strains. When fitted to the atomistic data, the simple rod model uses closed-form solutions for a cubic equation to predict the strain energy and morphology at a given twist angle and the crossover point between pure torsion and a helix. Our modeling and simulation bring key insights into the origin of the helical graphene morphologies stored inside of carbon nanotubes. They can be useful for designing chiral nanoribbons with tailored properties.

Ewald summation on a helix: A route to self-consistent charge density-functional based tight-binding objective molecular dynamics.

We explore the generalization to the helical case of the classical Ewald method, the harbinger of all modern self-consistent treatments of waves in crystals, including ab initio electronic structure methods. Ewald-like formulas that do not rely on a unit cell with translational symmetry prove to be numerically tractable and able to provide the crucial component needed for coupling objective molecular dynamics with the self-consistent charge density-functional based tight-binding treatment of the inter-atomic interactions. The robustness of the method in addressing complex hetero-nuclear nano- and bio-systems is demonstrated with illustrative simulations on a helical boron nitride nanotube, a screw dislocated zinc oxide nanowire, and an ideal DNA molecule.

A complete set of self-consistent charge density-functional tight-binding parametrization of zinc chalcogenides (ZnX; X=O, S, Se, and Te).

We have developed a complete set of self-consistent charge density-functional tight-binding parameters for ZnX (X = Zn, O, S, Se, Te, Cd, H, C, and N). The transferability of the derived parameters has been tested against Pseudo Potential-Perdew, Burke and Ernzerhof (PP-PBE) calculations and experimental values (whenever available) for corresponding bulk systems (e.g., hexagonal close packing, zinc-blende, and wurtzite(wz)), various kinds of nanostructures (such as nanowires, surfaces, and nanoclusters), and also some small molecular systems. Our results show that the derived parameters reproduce the structural and energetic properties of the above-mentioned systems very well. With the derived parameter set, one can study zinc-chalcogenide nanostructures of relatively large size which was otherwise prohibited by other methods. The Zn-Cd parametrization developed in this article will help in studying large semiconductor hetero-nanostructures of Zn and Cd chalcogenides such as ZnX/CdX core/shell nanoparticles, nanotubes, nanowires, and nanoalloys.

Dark states of single nitrogen-vacancy centers in diamond unraveled by single shot NMR.

The nitrogen-vacancy (NV) center in diamond is supposed to be a building block for quantum computing and nanometer-scale metrology at ambient conditions. Therefore, precise knowledge of its quantum states is crucial. Here, we experimentally show that under usual operating conditions the NV exists in an equilibrium of two charge states [70% in the expected negative (NV-) and 30% in the neutral one (NV0)]. Projective quantum nondemolition measurement of the nitrogen nuclear spin enables the detection even of the additional, optically inactive state. The nuclear spin can be coherently driven also in NV0 (T1≈90 ms and T2≈6 µs).

Self-Consistent-Charge Density-Functional Tight-Binding Parameters for Cd-X (X = S, Se, Te) Compounds and Their Interaction with H, O, C, and N.

Parameters for CdX, SeX, and TeX (X = H, C, N, O, S, Se, Te, and Cd) have been generated within the self-consistent-charge density-functional tight-binding (SCC-DFTB) framework. The approach has been tested against ab initio density-functional theory calculations for the relevant bulk phases, surfaces, nanowires, and small molecular systems. The SCC-DFTB approach reproduces structural, electronic, and energetic properties very well, demonstrating that the developed parameters are fully transferable among different chemical environments.

Optimal surface functionalization of silicon quantum dots.

Surface functionalization is a critical step for Si nanocrystals being used as biological probes and sensors. Using density-functional tight-binding calculations, we systematically investigate the optical properties of silicon quantum dots (SiQDs) with various termination groups, including H, CH(3), NH(2), SH, and OH. Our calculations reveal that capping SiQDs with alkyl group (-Si-C-) induces minimal changes in the optical spectra, while covering the surface with NH(2), SH, and OH results in evident changes compared to hydrogenated SiQDs. The structural deformations and electronic property changes due to surface passivation were shown to be responsible for the above-described features. Interestingly, we find that the optical properties of SiQDs can be controlled by varying the S coverage on the surface. This tuning effect may have important implications in device fabrications.

Resonant electron heating and molecular phonon cooling in single C60 junctions.

We study heating and heat dissipation of a single C(60) molecule in the junction of a scanning tunneling microscope by measuring the electron current required to thermally decompose the fullerene cage. The power for decomposition varies with electron energy and reflects the molecular resonance structure. When the scanning tunneling microscope tip contacts the fullerene the molecule can sustain much larger currents. Transport simulations explain these effects by molecular heating due to resonant electron-phonon coupling and molecular cooling by vibrational decay into the tip upon contact formation.

Analytical excited state forces for the time-dependent density-functional tight-binding method.

An analytical formulation for the geometrical derivatives of excitation energies within the time-dependent density-functional tight-binding (TD-DFTB) method is presented. The derivation is based on the auxiliary functional approach proposed in [Furche and Ahlrichs, J Chem Phys 2002, 117, 7433]. To validate the quality of the potential energy surfaces provided by the method, adiabatic excitation energies, excited state geometries, and harmonic vibrational frequencies were calculated for a test set of molecules in excited states of different symmetry and multiplicity. According to the results, the TD-DFTB scheme surpasses the performance of configuration interaction singles and the random phase approximation but has a lower quality than ab initio time-dependent density-functional theory. As a consequence of the special form of the approximations made in TD-DFTB, the scaling exponent of the method can be reduced to three, similar to the ground state. The low scaling prefactor and the satisfactory accuracy of the method makes TD-DFTB especially suitable for molecular dynamics simulations of dozens of atoms as well as for the computation of luminescence spectra of systems containing hundreds of atoms.

DFTB+, a sparse matrix-based implementation of the DFTB method.

A new Fortran 95 implementation of the DFTB (density functional-based tight binding) method has been developed, where the sparsity of the DFTB system of equations has been exploited. Conventional dense algebra is used only to evaluate the eigenproblems of the system and long-range Coulombic terms, but drop-in O(N) or O(N2) modules are planned to replace the small code sections that these entail. The developed sparse storage structure is discussed in detail, and a short overview of other features of the new code is given.

Self-interaction and strong correlation in DFTB.

The density functional based tight-binding (DFTB) method can benefit substantially from a number of developments in density functional theory (DFT) while also providing a simple analytical proving ground for new extensions. This contribution begins by demonstrating the variational nature of charge-self-consistent DFTB (SCC-DFTB), proving the presence of a defined ground-state in this class of methods. Because the ground state of the SCC-DFTB method itself can be qualitatively incorrect for some systems, suitable forms of the recent LDA+U functionals for SCC-DFTB are also presented. This leads to both a new semilocal self-interaction correction scheme and a new physical argument for the choice of parameters in the LDA+U method. The locality of these corrections can only partly repair the HOMO-LUMO gap and chemical potential discontinuity, hence a novel method for introducing this further physics into the method is also presented, leading to exact derivative discontinuities in this theory at low computational cost. The prototypical system NiO is used as an illustration for these developments.

Initial steps toward automating the fitting of DFTB Erep(r).

The most time-consuming part of developing new parametrizations for the density functional based tight-binding (DFTB) method consists of producing accurate and transferable repulsive pair potentials. In the conventional approach to repulsive parametrization, every possible diatomic combination of the elements covered by the parametrization must be individually hand-constructed. We present an initial attempt to automate some of this time-consuming process. We consider a simple genetic algorithm-based approach to the fitting problem.

An efficient LDA+U based tight binding approach.

The functionals usually applied in DFT calculations have deficiencies in describing systems with strongly localized electrons such as transition metals or rare earth (RE) compounds. In this work, we present the self-consistent charge density based functional tight binding (SCC-DFTB) calculation scheme including LDA+U like potentials and apply it for the simulation of RE-doped GaN. DFTB parameters for the simulation of GaN and a selection of rare earth ions, where the f electrons were explicitly included in the valence, have been created. The results of the simulations were tested against experimental data (where present) and against various more sophisticated but computationally more costly DFT calculations. Our approach is found to correctly reproduce the geometry and the energetic of the studied systems.

Theoretical Studies on Optical and Electronic Properties of Propionic-Acid-Terminated Silicon Quantum Dots.

The origin and stability of photoluminescence (PL) are critical issues for silicon nanoparticles to be used as biological probes. Optical and electronic properties of propionic-acid (PA) -terminated silicon quantum dots (SiQDs) were studied using the density-functional tight-binding method. We find that the adsorbed PA molecules slightly affect the structure of silicon core. The PA adsorption does not change the optical properties of SiQDs, while it substantially decreases the ionization potentials in the excited state and results in some new active orbitals with adjacent energies around the Fermi energy level. Accordingly, the modified surface of SiQDs can serve as a reaction substrate to oxygen and solvent molecules, which is responsible for the increase in both PL stability and water solubility.

Geometric and excited-state properties of 1,4-bis(benzothiazolylvinyl)benzene interacting with 2,2',2' '-(1,3,5-phenylene)tris[1-phenyl-1H-benzimidazole] studied by a density-functional tight-binding method.

The energetics and luminescent property of a guest molecule, 1,4-bis(benzothiazolylvinyl)benzene (BT), interacting with a host molecule, 2,2',2' '-(1,3,5-phenylene)tris[1-phenyl-1H-benzimidazole] (TPBI), in organic light-emitting diodes are studied by performing excited-state calculations using a time-dependent density-functional tight-binding method complemented with dispersion energy. It is found that the overlap between the TPBI emission and the BT absorption spectra shows an efficient energy transfer from the host molecule to the guest molecule when they are excited. The planar BT molecule becomes distorted when it is mixed with TPBI, resulting in a blue luminescence around 475 nm. The separation of the TPBI + BT mixture on a graphite surface is found to be energetically favorable, consistent with experimental observation.

Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps.

Motivated by the long-term goal of theoretically analyzing long-range proton transfer (PT) kinetics in biomolecular pumps, researchers made a number of technical developments in the framework of quantum mechanics-molecular mechanics (QM/MM) simulations. A set of collective reaction coordinates is proposed for characterizing the progress of long-range proton transfers; unlike previous suggestions, the new coordinates can describe PT along highly nonlinear three-dimensional pathways. Calculations using a realistic model of carbonic anhydrase demonstrated that adiabatic mapping using these collective coordinates gives reliable energetics and critical geometrical parameters as compared to minimum energy path calculations, which suggests that the new coordinates can be effectively used as reaction coordinate in potential of mean force calculations for long-range PT in complex systems. In addition, the generalized solvent boundary potential was implemented in the QM/MM framework for rectangular geometries, which is useful for studying reactions in membrane systems. The resulting protocol was found to produce water structure in the interior of aquaporin consistent with previous studies including a much larger number of explicit solvent and lipid molecules. The effect of electrostatics for PT through a membrane protein was also illustrated with a simple model channel embedded in different dielectric continuum environments. The encouraging results observed so far suggest that robust theoretical analysis of long-range PT kinetics in biomolecular pumps can soon be realized in a QM/MM framework.

Structures and energetics of hydrogen-terminated silicon nanowire surfaces.

The analysis and density-functional tight-binding simulations of possible configurations of silicon nanowires (SiNWs) enclosed by low-index surfaces reveal a number of remarkable features. For wires along <100>, <110>, and <111> directions, many low-index facet configurations and cross sections are possible, making their controlled growth difficult. The 112 wires are the most attractive for research and applications because they have only one configuration of enclosing low-index facets with a rectangular cross section, enclosed with the most stable (111) facet and the (110) facet next to it. In general, the stability of the SiNWs is determined by a balance between (1) minimization of the surface energy gamma(111)svr(rectangular)>svr(triangular)]. The energy band gaps follow the order of <100>wires > <112>wires > <111>wires > <110>wires. The results are compared with our recent scanning tunneling microscopy and transmission electron microscopy data.

Agglomeration of As antisites in As-rich low-temperature GaAs: nucleation without a critical nucleus size.

To investigate the early stages of nucleation and growth of As precipitates in GaAs grown at low substrate temperature, we make use of a self-consistent-charge density-functional based tight-binding method. Since a pair of As antisites already shows a significant binding energy which increases when more As antisites are attached, there is no critical nucleus size. Provided that all excess As has precipitated, the clusters may grow in size since the binding energies increase with increasing agglomeration size. These findings close the gap between experimental investigation of point defects and the detection of nanometer-size precipitates in transmission electron microscopy.