Structural and topological phase transitions induced by strain in two-dimensional bismuth.

We employ first-principles density-functional calculations to study structural and topological electronic transitions in two-dimensional bismuth layers. Our calculations reveal that a free-standing hexagonal bismuthene phase (the most stable one in the absence of strain) should become thermodinamically unstable against transformation to a putative 'pentaoctite' phase (composed entirely of pentagonal and octagonal rings), under biaxial tensile strain. Moreover, our results indicate that 2D bismuth layers in the pentaoctite phase should undergo a topological electronic phase transition under either a biaxial or uniaxial tensile strain. More specifically, at its equilibrium lattice parameters the pentaoctite lattice is a topologically trivial system with a direct band gap. Strain-induced parity inversion of valence and conduction bands is obtained, and the pentaoctite structure undergoes a transition to a topological-insulator phase at a biaxial tensile strain of 5%. In the case of uniaxial tensile strains, the topological transition happens at a tensile strain of 6% along the armchair direction of the pentaoctite lattice, and at a 5% tensile strain in the zigzag direction. Our study indicates that 2D bismuth layers may prove themselves a rich platform to realize topologically non-trivial 2D materials upon strain engineering.

Optical absorption in complexes of abasic DNA with noble-metal nanoclusters by first principles calculations.

Abasic sites (AP site) in a DNA duplex have been experimentally used to produce fluorescent Ag nanoclusters (NC) with a small number of atoms (n ≤ 6). These AP-DNA:NC complexes act as biological makers that help to locate genes associated with diseases related to single nucleotide polymorphisms (SNP), for example. Abasic sites are the most common SNP genetic variation, and their detection may help predict a host of genetically determined diseases. In this work, we report a theoretical study of the optical absorption spectra of AP-DNA:Ag4 and AP-DNA:Au4 complexes using a fully ab initio methodology. We consider several different base environments for the noble-metal nanocluster occupying the AP site, and compute the absorption spectra of sixteen AP-DNA:Ag4 and sixteen AP-DNA:Au4 complexes. We find that optical absorption in the AP-DNA:Ag4 complexes tends to concentrate in the green-to-violet range of frequencies (2.50 eV ≤ hω ≤ 3.2 eV) and that AP-DNA:Au4 complexes display absorption peaks in the violet-to-ultraviolet interval (hω ≥ 3.0 eV). An analysis of the optical absorption mechanisms in these complexes shows that they can be of local, charge-transfer, or hybrid nature, i.e., AP-DNA:NC complexes display the full variety of optical absorption processes in molecular systems. In particular, we identify both charge-transfer and hybrid processes involving several DNA bases surrounding the NC. Importantly, we find that even sequences where the Ag4 cluster is not in a guanine rich neighborhood display absorption peaks in the visible-light spectrum. Moreover, we obtain that the maximum intensities of the absorption peaks in complexes with pyrimidine vacancies are generally higher than those in complexes with purine vacancies. Regarding the selectivity of single-vacancy AP-DNA to specific noble-metal nanocluster sizes, our calculations show that the four-atom Ag4 (Au4) species fits naturally and binds into the AP-site in a single-vacancy AP-DNA.

Lubrication of Stone-Wales transformations in graphene by hydrogen and hydroxyl functional groups.

First-principles calculations were performed to address the role of functional groups (hydrogen atoms and hydroxyl molecules) in lubricating the fundamental transformation by which a Stone-Wales defect is formed in graphene. Energy barriers in the presence of a single H atom, as well as in the case of two, four, and six H atoms chemisorbed in graphene in several distinct site configurations are found to be smaller than in pristine graphene. Our study examines in detail the electronic mechanism behind the stabilization, by the functional groups, of the transition state of the defect-forming reaction relative to the reactants (functionalized graphene and Stone-Wales defect), due to partial strain relaxation and electronic saturation of the transition-state dangling bonds. We frame these findings in terms of the reactivity, to the functional groups, of the reactants and transition states. Our calculations point to a very favorable kinetic pathway with a strongly reduced activation barrier, in which two H atoms bind to next-nearest-neighbor C atoms, and saturate the two transition-state dangling bonds, resulting in a strong barrier reduction of 5.6 eV (from 9.3 eV without functional groups to 3.7 eV). In the case of two chemisorbed OH molecules, we find a further reduction of the Stone-Wales transformation barrier for one configuration considered, when compared to the similar one with two H atoms, providing additional confirmation of the reactivity-based mechanism.

Non-hexagonal-ring defects and structures induced by healing and strain in graphene and functionalized graphene.

We perform ab initio calculations for the strain-induced formation of non-hexagonal-ring defects in graphene, graphane (hydrogen-functionalized graphene) and graphenol (hydroxyl-functionalized graphene). We find that the simplest of such topological defects, the Stone-Wales defect, acts as a seed for strain-induced dissociation and multiplication of topological defects. Through the application of inhomogeneous deformations to graphene, graphane and graphenol with varying initial concentrations of pentagonal and heptagonal rings and small-sized voids, we obtain several novel stable structures that possess, at the same time, large concentrations of non-hexagonal rings (from fourfold to elevenfold) and small formation energies.

Correlated magnetic states in extended one-dimensional defects in graphene.

Ab initio calculations indicate that while the electronic states introduced by tilt grain boundaries in graphene are only partially confined to the defect core, a translational grain boundary introduces states near the Fermi level that are very strongly confined to the core of the defect, and display a ferromagnetic instability. The translational boundary lies along a graphene zigzag direction and its magnetic state is akin to that which has been theoretically predicted to occur on zigzag edges of graphene ribbons. Unlike ribbon edges, the translational grain boundary is fully immersed within the bulk of graphene, hence its magnetic state is protected from the contamination and reconstruction effects that have hampered experimental detection of the magnetic ribbon states. Moreover, our calculations suggest that charge transfer between grain boundaries and the bulk in graphene is short ranged, with charge redistribution confined to ~5 Å from the geometric center of the 1D defects.

Surface dangling-bond States and band lineups in hydrogen-terminated Si, Ge, and Ge/si nanowires.

We report an ab initio study of the electronic properties of surface dangling-bond (SDB) states in hydrogen-terminated Si and Ge nanowires with diameters between 1 and 2 nm, Ge/Si nanowire heterostructures, and Si and Ge (111) surfaces. We find that the charge transition levels epsilon(+/-) of SDB states behave as a common energy reference among Si and Ge wires and Si/Ge heterostructures, at 4.3+/-0.1 eV below the vacuum level. Calculations of epsilon(+/-) for isolated atoms indicate that this nearly constant value is a periodic-table atomic property.

Structures of Si and Ge nanowires in the subnanometer range.

We report an ab initio investigation of several structures of pristine Si and Ge nanowires with diameters between 0.5 and 2.0 nm. We consider nanowires based on the diamond structure, high-density bulk structures, and fullerenelike structures. Our calculations indicate a transition from sp3 geometries to structures with higher coordination, for diameters below 1.4 nm. We find that diamond-structure nanowires are unstable for diameters smaller than 1 nm, undergoing considerable structural transformations towards amorphouslike wires. For diameters between 0.8 and 1 nm, filled-fullerene wires are the most stable. For even smaller diameters (approximately 0.5 nm), we find that a simple hexagonal structure is particularly stable for both Si and Ge.

Stacking-fault based microscopic model for platelets in diamond.

We propose a new model for {001} platelets in diamond based on the formation of a metastable stacking-fault. The core of the defect is a double layer of threefold coordinated sp2 carbon atoms embedded in the sp3 diamond matrix. The properties of the model were determined using ab initio calculations. All significant experimental signatures attributed to the platelets are fully accounted for. The model is also very appealing from the point of view of kinetics, since naturally occurring shearing processes will lead to the formation of the metastable fault.