The SIESTA method; developments and applicability

Electrical and mechanical controlling of the kinetic and magnetic properties of hydrogen atoms on free-standing silicene

Effects of strain, charge doping and external electric field on kinetic and magnetic properties of hydrogen atoms on a free-standing silicene layer are investigated by first-principles density functional theory. It was found that the charge doping and strain are the most effective ways of changing the hydrogen-silicene binding energy, but they can only raise its value. The perpendicular external electric field can also lower it albeit in a narrower range. The strain has also the strongest impact on diffusion processes, and the diffusion barrier can be modified up to 50% of its unstrained value. The adsorption of hydrogen atoms results in a locally antiferromagnetic ground state with the effective exchange constant of approximately 1 eV. The system can easily be driven into a nonmagnetic phase by the charge doping and strain. The obtained results are very promising in view of the silicene functionalization and potential applications of silicene in fields of modern nanoelectronics and spintronics.

Optical response of silver clusters and their hollow shells from linear-response TDDFT

We present a study of the optical response of compact and hollow icosahedral clusters containing up to 868 silver atoms by means of time-dependent density functional theory. We have studied the dependence on size and morphology of both the sharp plasmonic resonance at 3-4 eV (originated mainly from sp-electrons), and the less studied broader feature appearing in the 6-7 eV range (interband transitions). An analysis of the effect of structural relaxations, as well as the choice of exchange correlation functional (local density versus generalised gradient approximations) both in the ground state and optical response calculations is also presented. We have further analysed the role of the different atom layers (surface versus inner layers) and the different orbital symmetries on the absorption cross-section for energies up to 8 eV. We have also studied the dependence on the number of atom layers in hollow structures. Shells formed by a single layer of atoms show a pronounced red shift of the main plasmon resonances that, however, rapidly converge to those of the compact structures as the number of layers is increased. The methods used to obtain these results are also carefully discussed. Our methodology is based on the use of localised basis (atomic orbitals, and atom-centered and dominant-product functions), which bring several computational advantages related to their relatively small size and the sparsity of the resulting matrices. Furthermore, the use of basis sets of atomic orbitals also allows the possibility of extending some of the standard population analysis tools (e.g. Mulliken population analysis) to the realm of optical excitations. Some examples of these analyses are described in the present work.

Two-Dimensional Phosphorus Carbide: Competition between sp(2) and sp(3) Bonding

We propose previously unknown allotropes of phosphorus carbide (PC) in the stable shape of an atomically thin layer. Different stable geometries, which result from the competition between sp(2) bonding found in graphitic C and sp(3) bonding found in black P, may be mapped onto 2D tiling patterns that simplify categorizing of the structures. Depending on the category, we identify 2D-PC structures that can be metallic, semimetallic with an anisotropic Dirac cone, or direct-gap semiconductors with their gap tunable by in-layer strain.

Van der Waals stacks of few-layer h-AlN with graphene: an ab initio study of structural, interaction and electronic properties

Graphite-like hexagonal AlN (h-AlN) multilayers have been experimentally manifested and theoretically modeled. The development of any functional electronics applications of h-AlN would most certainly require its integration with other layered materials, particularly graphene. Here, by employing vdW-corrected density functional theory calculations, we investigate structure, interaction energy, and electronic properties of van der Waals stacking sequences of few-layer h-AlN with graphene. We find that the presence of a template such as graphene induces enough interlayer charge separation in h-AlN, favoring a graphite-like stacking formation. We also find that the interface dipole, calculated per unit cell of the stacks, tends to increase with the number of stacked layers of h-AlN and graphene.

Riemann Surfaces of Carbon as Graphene Nanosolenoids

Traditional inductors in modern electronics consume excessive areas in the integrated circuits. Carbon nanostructures can offer efficient alternatives if the recognized high electrical conductivity of graphene can be properly organized in space to yield a current-generated magnetic field that is both strong and confined. Here we report on an extraordinary inductor nanostructure naturally occurring as a screw dislocation in graphitic carbons. Its elegant helicoid topology, resembling a Riemann surface, ensures full covalent connectivity of all graphene layers, joined in a single layer wound around the dislocation line. If voltage is applied, electrical currents flow helically and thus give rise to a very large (∼1 T at normal operational voltage) magnetic field and bring about superior (per mass or volume) inductance, both owing to unique winding density. Such a solenoid of small diameter behaves as a quantum conductor whose current distribution between the core and exterior varies with applied voltage, resulting in nonlinear inductance.

Rashba and Dresselhaus Effects in Hybrid Organic-Inorganic Perovskites: From Basics to Devices

We use symmetry analysis, density functional theory calculations, and k·p modeling to scrutinize Rashba and Dresselhaus effects in hybrid organic-inorganic halide perovskites. These perovskites are at the center of a recent revolution in the field of photovoltaics but have also demonstrated potential for optoelectronic applications such as transistors and light emitters. Due to a large spin-orbit coupling of the most frequently used metals, they are also predicted to offer a promising avenue for spin-based applications. With an in-depth inspection of the electronic structures and bulk lattice symmetries of a variety of systems, we analyze the origin of the spin splitting in two- and three-dimensional hybrid perovskites. It is shown that low-dimensional nanostructures made of CH3NH3PbX3 (X = I, Br) lead to spin splittings that can be controlled by an applied electric field. These findings further open the door for a perovskite-based spintronics.

Nanomesh-Type Graphene Superlattice on Au(111) Substrate

The adherence of graphene to various crystalline substrates often leads to a periodic out-of-plane modulation of its atomic structure due to the lattice mismatch. While, in principle, convex (protrusion) and concave (depression) superlattice geometries are nearly equivalent, convex superlattices have predominantly been observed for graphene on various metal surfaces. Here we report the STM observation of a graphene superlattice with concave (nanomesh) morphology on Au(111). DFT and molecular dynamics simulations confirm the nanomesh nature of the graphene superlattice on Au(111) and also reveal its potential origin as a surface reconstruction, consisting of the imprinting of the nanomesh morphology into the Au(111) surface. This unusual surface reconstruction can be attributed to the particularly large mobility of the Au atoms on Au(111) surfaces and most probably plays an important role in stabilizing the concave graphene superlattice. We report the simultaneous observation of both convex and concave graphene superlattices on herringbone reconstructed Au(111) excluding the contrast inversion as the origin of the observed concave morphology. The observed graphene nanomesh superlattice can provide an intriguing nanoscale template for self-assembled structures and nanoparticles that cannot be stabilized on other surfaces.

Mechanisms of formation of chemical bonding and defect formation at the a-SiO2/BaTiO3 interfaces

The structure and mechanisms of bonding and defect formation at the interfaces between amorphous silica (a-SiO2) and BaTiO3(0 0 1) were investigated using ab initio molecular dynamics. It was found that the nature of interfacial bonds crucially depends on the BaTiO3 surface termination. In particular, the interface between silica and TiO2-terminated BaTiO3 (BTO) slab is characterised by strong covalent Ti-O-Si bonds, while the interface between silica and BaO-terminated BTO demonstrates ionic character of interfacial bonds and exhibits bond instability. In both cases, the dynamics of oxygen species at oxide interfaces is a driving force of the formation of interfacial bonds and defects.

Structural and electronic control of the metal to insulator transition and local orderings in the θ-(BEDT-TTF)2X organic conductors

A first-principles density functional theory (DFT) study of [Formula: see text]-(BEDT-TTF)2X molecular conductors with X  =  I3, CsCo(SCN)4 (ambient pressure, 7.5 kbar and 10 kbar), CsZn(SCN)4, TlCo(SCN)4, RbCo(SCN)4 and RbZn(SCN)4 (220 K and 90 K) is reported. It is shown that these salts exhibit three different types of band structure each of them associated with a different physical behavior. In contrast with previous proposals it is found that the key electronic parameter behind the differences in the band structures is the intrastack transfer integral, t c . A new mechanism for the metal to insulator transition in the [Formula: see text]-(BEDT-TTF)2MM'(SCN)4 ([Formula: see text], Tl; [Formula: see text], Co) salts is proposed, where an order-disorder structural transition of the ethylenedithio groups doubling the periodicity along the stack direction drives the system into an electronically pseudo-1D system along the interstack direction that is subject to a 4k F charge localization of holes. The structural rearrangement is such that the holes are not distributed equally between the two donors; the larger hole density is associated with the B donors which establish the strongest hydrogen bonds with the anion layers. A detailed microscopic description of how disorder of the ethylenedithio groups, the θ dihedral angle and the electronic structure intermingle and lead to the unusual phase diagram of these salts is presented. In this framework the role of pressure and uniaxial strain in controlling the physical behavior of these salts is discussed.

Elucidating the fundamental forces in protein crystal formation: the case of crambin

This study demonstrates the feasibility of periodic all-electron hybrid density functional theory calculations in the description of protein crystals, using crambin as a test case.

Molecular simulations of proteins have been usually accomplished through empirical or semi-empirical potentials, due to the large size and inherent complexity of these biological systems. On the other hand, a theoretical description of proteins based on quantum-mechanical methods would however provide an unbiased characterization of their electronic properties, possibly offering a link between these and the ultimate biological activity. Yet, such approaches have been historically hindered by the large amount of requested computational power. Here we demonstrate the feasibility of periodic all-electron density functional theory calculations in the description of the crystal of the protein crambin (46 aminoacids), which is determined with exceptional structural accuracy. We have employed the hybrid B3LYP functional, coupled to an empirical description of London interactions (D*) to simulate the crambin crystal with an increasing amount of lattice water molecules in the cell (up to 172H₂O per cell). The agreement with the experiment is good for both protein geometry and protein–water interactions. The energetics was computed to predict crystal formation energies, protein–water and protein–protein interaction energies. We studied the role of dispersion interactions which are crucial for holding the crambin crystal in place. B3LYP-D* electrostatic potential and dipole moment of crambin as well as the electronic charge flow from crambin to the solvating water molecules (0.0015e per H₂O) have also been predicted. These results proved that quantum-mechanical simulations of small proteins, both free and in their crystalline state, are now feasible in a reasonable amount of time, by programs capable of exploiting high performance computing architectures, allowing the study of protein properties not easily amenable through classical force fields.

The determining factor of a preferred orientation of GaN domains grown on m-plane sapphire substrates

Epitaxial lateral overgrowth in tandem with the first-principles calculation was employed to investigate the determining factor of a preferred orientation of GaN on SiO2-patterned m-plane sapphire substrates. We found that the (100)-orientation is favored over the (10)-orientation in the region with a small filling factor of SiO₂, while the latter orientation becomes preferred in the region with a large filling factor. This result suggests that the effective concentration determines the preferred orientation of GaN: the (100)- and (10)-orientations preferred at their low and high concentrations, respectively. Our computational study revealed that at a low coverage of Ga and N atoms, the local atomic arrangement resembles that on the (10) surface, although the (100) surface is more stable at their full coverage. Such a (10)-like atomic configuration crosses over to the local structure resembling that on the (100) surface as the coverage increases. Based on results, we determined that high effective concentration of Ga and N sources expedites the growth of the (10)-orientation while keeping from transition to the (100)-orientation. At low effective concentration, on the other hand, there is a sufficient time for the added Ga and N sources to rearrange the initial (10)-like orientation to form the (100)-orientation.

Intrinsic Defects, Fluctuations of the Local Shape, and the Photo-Oxidation of Black Phosphorus

Black phosphorus is a monatomic semiconducting layered material that degrades exothermically in the presence of light and ambient contaminants. Its degradation dynamics remain largely unknown. Even before degradation, local-probe studies indicate non-negligible local curvature-through a nonconstant height distribution-due to the unavoidable presence of intrinsic defects. We establish that these intrinsic defects are photo-oxidation sites because they lower the chemisorption barrier of ideal black phosphorus (>10 eV and out of visible-range light excitations) right into the visible and ultraviolet range (1.6 to 6.8 eV), thus enabling photoinduced oxidation and dissociation of oxygen dimers. A full characterization of the material's shape and of its electronic properties at the early stages of the oxidation process is presented as well. This study thus provides fundamental insights into the degradation dynamics of this novel layered material.

Structural Transition in Layered As(1-x)P(x) Compounds: A Computational Study

As a way to further improve the electronic properties of group V layered semiconductors, we propose to form in-layer 2D heterostructures of black phosphorus and gray arsenic. We use ab initio density functional theory to optimize the geometry, determine the electronic structure, and identify the most stable allotropes as a function of composition. Because pure black phosphorus and pure gray arsenic monolayers differ in their equilibrium structure, we predict a structural transition and a change in frontier states, including a change from a direct-gap to an indirect-gap semiconductor, with changing composition.

Designing Isoelectronic Counterparts to Layered Group V Semiconductors

In analogy to III-V compounds, which have significantly broadened the scope of group IV semiconductors, we propose a class of IV-VI compounds as isoelectronic counterparts to layered group V semiconductors. Using ab initio density functional theory, we study yet unrealized structural phases of silicon monosulfide (SiS). We find the black-phosphorus-like α-SiS to be almost equally stable as the blue-phosphorus-like β-SiS. Both α-SiS and β-SiS monolayers display a significant, indirect band gap that depends sensitively on the in-layer strain. Unlike 2D semiconductors of group V elements with the corresponding nonplanar structure, different SiS allotropes show a strong polarization either within or normal to the layers. We find that SiS may form both lateral and vertical heterostructures with phosphorene at a very small energy penalty, offering an unprecedented tunability in structural and electronic properties of SiS-P compounds.

Systematic pseudopotentials from reference eigenvalue sets for DFT calculations: Pseudopotential files

We present in this article a pseudopotential (PP) database for DFT calculations in the context of the SIESTA code [1-3]. Comprehensive optimized PPs in two formats (psf files and input files for ATM program) are provided for 20 chemical elements for LDA and GGA exchange-correlation potentials. Our data represents a validated database of PPs for SIESTA DFT calculations. Extensive transferability tests guarantee the usefulness of these PPs.

Effects of stoichiometric doping in superconducting Bi-O-S compounds

Newly discovered Bi-O-S compounds remain an enigma in attempts to understand their electronic properties. A recent study of Bi4O4S3 has shown it to be a mixture of two phases, Bi2OS2 and Bi3O2S3, the latter being superconducting (Phelan et al 2013 J. Am. Chem. Soc. 135 5372-4). Using density functional theory, we explore the electronic structure of both the phases and the effect of the introduction of extra BiS2 bilayers. Our results demonstrate that the S2 layers dope the bismuth-sulphur bands and this causes metallisation. The bands at the Fermi level are of clear two-dimensional character. One band manifold is confined to the two adjacent, square-lattice bismuth-sulphur planes, a second manifold is confined to the square lattice of sulphur dimers. We show that the introduction of extra BiS2 bilayers does not influence the electronic structure. Finally, we also show that spin-orbit coupling does not have any significant effect on the states close to the Fermi level at the energy scale considered.

Undercover diffusion of atoms: Pb on Si(5 5 3)-Au surface covered by graphene

The diffusion of Pb atoms under a graphene layer deposited on a Si(5 5 3)-Au surface is studied by the first-principles density functional theory. The presence of graphene locks the moving Pb atoms inside tube-like closed objects, formed by grooves near steps of the Si(5 5 3)-Au surface and limited from the top by the graphene layer. As a result, the diffusion processes are well-separated from the environment. The methods of experimental verification of the undercover diffusion are also proposed.

Nanomechanics of bidentate thiolate ligands on gold surfaces

The effect of the chain length separating sulfur atoms in bidentate thiols attached to defective gold surfaces on the rupture of the respective molecule-gold junctions has been studied computationally. Thermal desorption always yields cyclic disulfides. In contrast, mechanochemical desorption leads to cyclic gold complexes, where metal atoms are extracted from the surface and kept in tweezer-like arrangements by the sulfur atoms. This phenomenon is rationalized in terms of directional mechanical manipulation of Au-Au bonds and Au-S coordination numbers. Moreover, the flexibility of the chain is shown to crucially impact on the mechanical strength of the junction.

Monoxides of small terbium clusters: a density functional theory investigation

To investigate the effect of oxygen atom on the geometrical structures, electronic, and magnetic properties of small terbium clusters, we carried out the first-principles calculations on TbnO (n = 1-14) clusters. The capping of an oxygen atom on one trigonal-facet of Tbn structures is always favored energetically, which can significantly improve the structural stability. The far-infrared vibrational spectroscopies are found to be different from those of corresponding bare clusters, providing a distinct signal to detect the characteristic structures of TbnO clusters. The primary effect of oxygen atom on magnetic properties is to change the magnetic orderings among Tb atoms and to reduce small of local magnetic moments of the O-coordinated Tb atoms, both of which serve as the key reasons for the experimental magnetic evolution of an oscillating behavior. These calculations are consistent with, and help to account for, the experimentally observed magnetic properties of monoxide TbnO clusters [C. N. Van Dijk et al., J. Appl. Phys. 107, 09B526 (2010)].

Tiling phosphorene

We present a scheme to categorize the structure of different layered phosphorene allotropes by mapping their nonplanar atomic structure onto a two-color 2D triangular tiling pattern. In the buckled structure of a phosphorene monolayer, we assign atoms in "top" positions to dark tiles and atoms in "bottom" positions to light tiles. Optimum sp3 bonding is maintained throughout the structure when each triangular tile is surrounded by the same number N of like-colored tiles, with 0≤N≤2. Our ab initio density functional calculations indicate that both the relative stability and electronic properties depend primarily on the structural index N. The proposed mapping approach may also be applied to phosphorene structures with nonhexagonal rings and 2D quasicrystals with no translational symmetry, which we predict to be nearly as stable as the hexagonal network.

High Stability of Faceted Nanotubes and Fullerenes of Multiphase Layered Phosphorus: A Computational Study

We present a paradigm in constructing very stable, faceted nanotube and fullerene structures by laterally joining nanoribbons or patches of different planar phosphorene phases. Our ab initio density functional calculations indicate that these phases may form very stable, nonplanar joints. Unlike fullerenes and nanotubes obtained by deforming a single-phase planar monolayer at substantial energy penalty, we find faceted fullerenes and nanotubes to be nearly as stable as the planar single-phase monolayers. The resulting rich variety of polymorphs allows us to tune the electronic properties of phosphorene nanotubes and fullerenes not only by the chiral index but also by the combination of different phosphorene phases. In selected phosphorene nanotubes, a metal-insulator transition may be induced by strain or by changing the number of walls.

Spin transport in dangling-bond wires on doped H-passivated Si(100)

New advances in single-atom manipulation are leading to the creation of atomic structures on H-passivated Si surfaces with functionalities important for the development of atomic and molecular based technologies. We perform total-energy and electron-transport calculations to reveal the properties and understand the features of atomic wires crafted by H removal from the surface. The presence of dopants radically change the wire properties. Our calculations show that dopants have a tendency to approach the dangling-bond wires, and in these conditions, transport is enhanced and spin selective. These results have important implications in the development of atomic-scale spintronics showing that boron, and to a lesser extent phosphorous, convert the wires in high-quality spin filters.

Tunable magnetic and electronic properties of BN nanosheets with triangular defects: a first-principles study

Experimentally, vacancy defects are commonly observed in BN nanosheets, expecially nitrogen-terminated triangular defects. Based on first-principles calculations, we systematically investigate the magnetic and electronic properties of BN nanosheets with these triangular vacancies (referred to as Vi(i = 1 - 4) defects with i representing the number of N atoms on each side of the triangle). It is found that the Vi defects bring diverse magnetic states into BN sheets, which are ferrimagnetic for V1, nonmagnetic for V2, ferrimagnetic for V3 and antiferromagnetic for V4 defects. When the isotropic strains are applied, the ferrimagnetic state is sustained for V1 defect, whereas the V2 defect undergoes a nonmagnetic to antiferromagnetic transition and the V3, V4 defects experience an abrupt change in the absolute magnetic moments under small strains, which are originated from the N-N bond breaking at these defects. Different from the BN nanoribbons, the antiparallel coupling is more favorable for the N atoms at the edges of triangular defects. Due to the triangular defects, the band gaps of BN sheets are reduced substantially, which could be further modulated by the strains. When the defective BN sheets serve as a substrate for graphene, the V1, V3 and V4 defects in BN would induce p-type doping in the graphene sheet. Interestingly, when the V2 defect is embedded in BN sheets, the doping behavior of graphene can be well-controlled by the strain, which is charge neutral at the strain-free state and p-type doped under strains. Our studies demonstrate that the rich magnetic and electronic properties of BN sheets with triangular defects enable the system's potential applications in nanodevices.

Ab initio electronic properties of dual phosphorus monolayers in silicon

IN THE MIDST OF THE EPITAXIAL CIRCUITRY REVOLUTION IN SILICON TECHNOLOGY, WE LOOK AHEAD TO THE NEXT PARADIGM SHIFT: effective use of the third dimension - in particular, its combination with epitaxial technology. We perform ab initio calculations of atomically thin epitaxial bilayers in silicon, investigating the fundamental electronic properties of monolayer pairs. Quantitative band splittings and the electronic density are presented, along with effects of the layers' relative alignment and comments on disordered systems, and for the first time, the effective electronic widths of such device components are calculated.

Phase coexistence and metal-insulator transition in few-layer phosphorene: a computational study

Based on ab initio density functional calculations, we propose γ-P and δ-P as two additional stable structural phases of layered phosphorus besides the layered α-P (black) and β-P (blue) phosphorus allotropes. Monolayers of some of these allotropes have a wide band gap, whereas others, including γ-P, show a metal-insulator transition caused by in-layer strain or changing the number of layers. An unforeseen benefit is the possibility to connect different structural phases at no energy cost. This becomes particularly valuable in assembling heterostructures with well-defined metallic and semiconducting regions in one contiguous layer.

Semiconducting layered blue phosphorus: a computational study

We investigate a previously unknown phase of phosphorus that shares its layered structure and high stability with the black phosphorus allotrope. We find the in-plane hexagonal structure and bulk layer stacking of this structure, which we call "blue phosphorus," to be related to graphite. Unlike graphite and black phosphorus, blue phosphorus displays a wide fundamental band gap. Still, it should exfoliate easily to form quasi-two-dimensional structures suitable for electronic applications. We study a likely transformation pathway from black to blue phosphorus and discuss possible ways to synthesize the new structure.

Conducting linear chains of sulphur inside carbon nanotubes

Despite extensive research for more than 200 years, the experimental isolation of monatomic sulphur chains, which are believed to exhibit a conducting character, has eluded scientists. Here we report the synthesis of a previously unobserved composite material of elemental sulphur, consisting of monatomic chains stabilized in the constraining volume of a carbon nanotube. This one-dimensional phase is confirmed by high-resolution transmission electron microscopy and synchrotron X-ray diffraction. Interestingly, these one-dimensional sulphur chains exhibit long domain sizes of up to 160 nm and high thermal stability (~800 K). Synchrotron X-ray diffraction shows a sharp structural transition of the one-dimensional sulphur occurring at ~450-650 K. Our observations, and corresponding electronic structure and quantum transport calculations, indicate the conducting character of the one-dimensional sulphur chains under ambient pressure. This is in stark contrast to bulk sulphur that needs ultrahigh pressures exceeding ~90 GPa to become metallic.

Topologically protected conduction state at carbon foam surfaces: an ab initio study

We report results of ab initio electronic structure and quantum conductance calculations indicating the emergence of conduction at the surface of semiconducting carbon foams. The occurrence of new conduction states is intimately linked to the topology of the surface and not limited to foams of elemental carbon. Our interpretation based on rehybridization theory indicates that conduction in the foam derives from first- and second-neighbor interactions between p∥ orbitals lying in the surface plane, which are related to p⊥ orbitals of graphene. The topologically protected conducting state occurs on bare and hydrogen-terminated foam surfaces and is thus unrelated to dangling bonds. Our results for carbon foam indicate that the conductance behavior may be further significantly modified by surface patterning.

Voltage tuning of vibrational mode energies in single-molecule junctions

Vibrational modes of molecules are fundamental properties determined by intramolecular bonding, atomic masses, and molecular geometry, and often serve as important channels for dissipation in nanoscale processes. Although single-molecule junctions have been used to manipulate electronic structure and related functional properties of molecules, electrical control of vibrational mode energies has remained elusive. Here we use simultaneous transport and surface-enhanced Raman spectroscopy measurements to demonstrate large, reversible, voltage-driven shifts of vibrational mode energies of C60 molecules in gold junctions. C60 mode energies are found to vary approximately quadratically with bias, but in a manner inconsistent with a simple vibrational Stark effect. Our theoretical model instead suggests that the mode shifts are a signature of bias-driven addition of electronic charge to the molecule. These results imply that voltage-controlled tuning of vibrational modes is a general phenomenon at metal-molecule interfaces and is a means of achieving significant shifts in vibrational energies relative to a pure Stark effect.

Electronic transport in patterned graphene nanoroads

Graphane, hydrogenated graphene, can be patterned into electronic devices by selectively removing hydrogen atoms. The most simple of such devices is the so-called nanoroad, analogous to the graphene nanoribbon, where confinement-and the opening of a gap-is obtained without the need for breaking the carbon bonds. In this work we address the electronic transport properties of such systems considering different hydrogen impurities within the conduction channel. We show, using a combination of density functional theory and non-equilibrium Green's functions, that hydrogen leads to significant changes in the transport properties and in some cases to current polarization.

Density functional theory in materials science

Materials science is a highly interdisciplinary field. It is devoted to the understanding of the relationship between (a) fundamental physical and chemical properties governing processes at the atomistic scale with (b) typically macroscopic properties required of materials in engineering applications. For many materials, this relationship is not only determined by chemical composition, but strongly governed by microstructure. The latter is a consequence of carefully selected process conditions (e.g., mechanical forming and annealing in metallurgy or epitaxial growth in semiconductor technology). A key task of computational materials science is to unravel the often hidden composition-structure-property relationships using computational techniques. The present paper does not aim to give a complete review of all aspects of materials science. Rather, we will present the key concepts underlying the computation of selected material properties and discuss the major classes of materials to which they are applied. Specifically, our focus will be on methods used to describe single or polycrystalline bulk materials of semiconductor, metal or ceramic form.

Mechanically controllable bi-stable states in a highly conductive single pyrazine molecular junction

We report the fabrication of a highly conductive single pyrazine molecular junction with Pt leads. Mechanically controllable break-junction measurements at low temperatures show two distinct high and low conductance states. These conductance values are two orders of magnitude larger than those of a conventional single molecular junction with anchoring groups because of direct binding of the π conjugated molecule to a metal electrode with large density of states at the Fermi energy. Inelastic electron tunneling spectroscopy combined with density functional theory calculations highlights the vibration modes of the system for the two regimes. Theory allows us to assign the high and low conductance states of the molecular junction to two configurations in which the pyrazine axis is tilted and parallel with respect to the junction axis, respectively. Finally, we show that the pyrazine junction can be reversibly switched between the two bi-stable conductance states by mechanically stretching and relaxing the junction.

Structure and magnetism of disordered carbon

Motivated by the observation of ferromagnetism in carbon foams, we perform a massive search for (meta)stable disordered structures of elemental carbon by a generate and test approach. We use the density functional based program SIESTA to optimize the structures and calculate the electronic spectra and spin densities. About 1% of the 24,000 optimized structures present magnetic moments, a necessary but not sufficient condition for intrinsic magnetic order. We analyse the results using elements of graph theory. Although the relation between the structure and the occurrence of magnetic moments is not yet fully clarified, we give some minimal requirements for this possibility, such as the existence of three-fold coordinated atoms surrounded by four-fold coordinated atoms. We discuss in detail the most promising structures.

Identification of vibrational signatures from short chains of interlinked molecule-nanoparticle junctions obtained by inelastic electron tunnelling spectroscopy

Short chains containing a series of metal-molecule-nanoparticle nanojunctions are a nano-material system with the potential to give electrical signatures close to those from single molecule experiments while enabling us to build portable devices on a chip. Inelastic electron tunnelling spectroscopy (IETS) measurements provide one of the most characteristic electrical signals of single and few molecules. In interlinked molecule-nanoparticle (NP) chains containing typically 5-7 molecules in a chain, the spectrum is expected to be a superposition of the vibrational signatures of individual molecules. We have established a stable and reproducible molecule-AuNP multi-junction by placing a few 1,8-octanedithiol (ODT) molecules onto a versatile and portable nanoparticle-nanoelectrode platform and measured for the first time vibrational molecular signatures at complex and coupled few-molecule-NP junctions. From quantum transport calculations, we model the IETS spectra and identify vibrational modes as well as the number of molecules contributing to the electron transport in the measured spectra.

Spin-polarized transport through single-molecule magnet Mn6 complexes

The coherent transport properties of a device, constructed by sandwiching a Mn6 single-molecule magnet between two gold surfaces, are studied theoretically by using the non-equilibrium Green's function approach combined with density functional theory. Two spin states of such Mn6 complexes are explored, namely the ferromagnetically coupled configuration of the six Mn(III) cations, leading to the S = 12 ground state, and the low S = 4 spin state. For voltages up to 1 volt the S = 12 ground state shows a current one order of magnitude larger than that of the S = 4 state. Furthermore this is almost completely spin-polarized, since the Mn6 frontier molecular orbitals for S = 12 belong to the same spin manifold. As such the high-anisotropy Mn6 molecule appears as a promising candidate for implementing, at the single molecular level, both spin-switches and low-temperature spin-valves.