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Our analysis based on the results of hybrid and semilocal density-functional calculations with and without Hubbard U correction for on-site Coulomb interactions reveals the true magnetic ground states of three transition-metal dichalcogenide monolayers, viz., FeTe2,VS2, and NiTe2, which comprise inhomogeneous magnetic moment configurations. In contrast to earlier studies considering only the magnetic moments of transition-metal atoms, the chalcogen atoms by themselves have significant, antiparallel magnetic moments owing to the spin polarization through p−d hybridization. The latter is found to be true for both H and T phases of FeTe2,VS2, and NiTe2 monolayers. Our predictions show that the FeTe2 monolayer in its lowest-energy structure is a half metal, which prevails under both compressive and tensile strains. Half metallicity occurs also in the FeTe2 bilayer but disappears in thicker multilayers. The VS2 monolayer is a magnetic semiconductor; it has two different band gaps of different character and widths for different spin polarization. The NiTe2 monolayer, which used to be known as a nonmagnetic metal, is indeed a magnetic metal with a small magnetic moment. These monolayers with intriguing electronic and magnetic properties can attain new functionalities for spintronic applications.

Interaction between two surfaces in relative motion can give rise to energy dissipation and hence sliding friction. A significant portion of the energy is dissipated through the creation of non-equilibrium phonons. Recent advances in material synthesis have made the production of specific single layer honeycomb structures and their multilayer phases, such as graphene, graphane, fluorographene, MoS2 and WO2. When coated to the moving surfaces, the attractive interaction between these layers is normally very weak and becomes repulsive at large separation under loading force. Providing a rigorous quantum mechanical treatment for the 3D sliding motion under a constant loading force within Prandtl-Tomlinson model, we derive the critical stiffness required to avoid stick-slip motion. Also these nanostructures acquire low critical stiffness even under high loading force due to their charged surfaces repelling each other. The intrinsic stiffness of these materials exceeds critical stiffness and thereby thematerials avoid stick-slip regime and attain nearly dissipationless continuous sliding. Remarkably, layered WO2 a much better performance as compared to others and promises a potential superlubricant nanocoating. The absence of mechanical instabilities leading to conservative lateral forces is also confirmed directly by the simulations of sliding layers. Graphene coated metal surfaces also attain superlubricity and hence nearly frictionless sliding through a charge exchange mechanism with metal surface. © Springer International Publishing Switzerland 2015.

The growth of the 3√×3√ reconstructed silicene on Ag substrate has been frequently observed in experiments while its atomic structure and formation mechanism is poorly understood. Here, by first-principles calculations, we show that 3√×3√ reconstructed silicene is constituted by dumbbell units of Si atoms arranged in a honeycomb pattern. Our model shows excellent agreement with the experimentally reported lattice constant and STM image. We propose a new mechanism for explaining the spontaneous and consequential formation of 3√×3√ structures from 3×3 structures on Ag substrate. We show that the 3√×3√ reconstruction is mainly determined by the interaction between Si atoms and have weak influence from Ag substrate. The proposed mechanism opens the path to understanding of multilayer silicon. ©2014 American Physical Society

With the synthesis of a single atomic plane of graphite, namely, graphene honeycomb structure, a new perspective for carbon-based electronics is opened. The one-dimensional graphene nanoribbons (GNRs) have different band-gap values depending on their edge shape and width. In this contribution, we report our results showing that repeated heterostructures of GNRs of different widths form multiple quantum-well structures. The widths of the constituent parts as well as the bandgap, and also the magnetic ground state of the superlattices are modulated in direct space. We provide detailed analysis of these structures and show that superlattices with armchair edge shapes can be used as resonant tunneling devices and those with zigzag edge shape have unique features for spintronic applications. We also discuss another route of functionalizing 2D graphene, 1D GNR, and superlattices with 3d-transition metal (TM) atom adsorption. © Springer-Verlag Berlin Heidelberg 2013.

Based on first-principles density functional theory and finite temperature molecular dynamics calculations, we predict that H 2O can be dissociated into its constituents O and H at specific vacancy defects of single-layer MoS 2 honeycomb structure, which subsequently are bound to fourfolded Mo and twofolded S atoms surrounding the vacancy, respectively. This exothermic and spontaneous process occurs, since the electronegativity and ionization energy of Mo are smaller than those of H. Once desorbed from twofolded S atoms, H atoms migrate readily on the MoS 2 surface and eventually form free H 2 molecules to be released from the surface. Present results are critical for acquiring clean and sustainable energy from hydrogen. © 2012 American Physical Society.

We investigate the hydrogen absorption capacity of two tubular structures, namely, B Be -substituted single-wall carbon nanotube (SWNT) and Ti covered single-wall boron nitride nanotube (SWBNT) using first-principles plane wave method. The interaction of H2 molecules with the outer surface of bare SWBNT, which is normally very weak, can be significantly enhanced upon functionalization by Ti atoms. Each Ti atom adsorbed on SWBNT can bind up to four H2 molecules with an average binding energy suitable for room temperature storage. While the substitution process of Be atom on SWNT is endothermic, the substituted Be strengthens the interaction between tube surface and H2 to hold one H2 molecule. © 2007 The American Physical Society.

Mechanical properties, atomic and energy band structures of bare and hydrogen-passivated Sin Gen nanowire superlattices have been investigated by using first-principles pseudopotential plane-wave method. Undoped, tetrahedral Si and Ge nanowire segments join pseudomorphically and can form superlattice with atomically sharp interface. We found that Sin nanowires are stiffer than Gen nanowires. Hydrogen passivation makes these nanowires and Sin Gen nanowire superlattice even more stiff. Upon heterostructure formation, superlattice electronic states form subbands in momentum space. Band lineups of Si and Ge zones result in multiple quantum wells, where specific states at the band edges and in band continua are confined. The electronic structure of the nanowire superlattice depends on the length and cross section geometry of constituent Si and Ge segments. Since bare Si and Ge nanowires are metallic and the band gaps of hydrogenated ones vary with the diameter, Sin Gen superlattices offer numerous alternatives for multiple quantum well devices with their leads made from the constituent metallic nanowires.

Electronic and atomic structures of the clean and As- and Te-covered Si(211) surface are studied using pseudopotential density-functional method. The clean surface is found to have (2 x 1) and rebonded (1 x 1) reconstructions as stable surface structures, but no π-bonded chain reconstruction. Binding energies of As and Te adatoms at a number of symmetry sites on the ideal and (2 x 1) reconstructed surfaces have been calculated because of their importance in the epitaxial growth of CdTe and other materials on the Si(211) surface. The special symmetry sites on these surfaces having the highest binding energies for isolated As and Te adatoms are identified. But more significantly, several sites are found to be nearly degenerate in binding-energy values. This has important consequences for epitaxial growth processes. Optimal structures calculated for 0.5 monolayer of As and Te coverage reveal that the As adatoms dimerize on the surface while the Te adatoms do not. However, both As- and Te-covered surfaces are found to be metallic in nature.

During epitaxial growth of semiconducting materials using either molecular beam epitaxy or organometallic vapour deposition, the addition of a surfactant can enhance two-dimensional layer-by-layer growth. This modified growth process is now called the surfactant-mediated growth (SMG) method. It has had an important impact on the development of technologically important materials in device applications, such as heterostructures used for laser applications. Recent developments that use surfactants to improve doping profiles in semiconducting systems and antisurfactants (ASMG) to grow quantum dots further ensure that SMG/ASMG will play a major role in the future development of optoelectronic materials and nanoparticles. In this paper, we review important earlier experimental work involving the SMG method as well as some recent developments. Theoretical work involving first-principles methods and kinetic Monte Carlo simulations are discussed but confined only to the surfactant effect.

We perform first principles density functional calculations to investigate the adsorption of Te on the Si(0 0 1) surface from low coverage up to a monolayer coverage. At low coverage, a Te atom is adsorbed on top of the Si surface dimer bond. At higher coverages, Te atoms adsorption causes the Si-Si dimer bond to break, lifting the (2 × 1) reconstruction. We find no evidence of the Te-Te dimer bond formation as a possible source of the (2 × 1) reconstruction at a monolayer coverage. Finite temperature ab initio molecular dynamics calculations show that Te covered Si(0 0 1) surfaces do not have any definitive reconstruction. Vibrations of the bridged Te atoms in the strongly anharmonic potentials prevent the reconstruction structure from attaining any permanent, two-dimensional periodic geometry. This explains why experiments attempting to find a definite model for the reconstruction reached conflicting conclusions. © 2002 Elsevier Science B.V. All rights reserved.

We present a formalism for an atomic scale study of phononic heat transfer. The expression of thermal energy current can be cast in the Landauer form and incorporates the transmission coefficient explicitly. Calculation of the thermal conductance of a monoatomic chain of N atoms between two reservoirs shows interesting quantum features. The conductance density appears as Lorentzian type resonances at the eigenfrequencies of the chain. At low-temperature limit the discrete vibrational frequency spectrum of a "soft" chain may reflect on the thermal conductance by giving rise to a sudden increase. At room temperature, the conductance through a "stiff" chain may oscillate with the number of chain atoms. The obtained quantum features are compared with similar effects found in the quantized electrical conductance.

Nanowires, point contacts and metallic single-wall carbon nanotubes are one-dimensional nanostructures which display important size-dependent quantum effects. Quantization due to the transverse confinement and resultant finite level spacing of electronic and phononic states are responsible for some novel effects. Many studies have revealed fundamental and technologically important properties, which are being explored for fabricating future nanodevices. Various simulation studies based on the classical molecular dynamics method and combined force and current measurements have shown the relationship between atomic structure and transport properties. The atomic, electronic and transport properties of these nanostructures have been an area of active research. This brief review presents some quantum effects in the electronic and phononic transport through nanowires.

We present a first-principles study to elucidate the nature of the bonding, stability, energetics, and dynamics of individual X8H8 molecules (X = C, Si, Ge). The results obtained from both "local basis" and "pseudopotential" ab initio methods are in good agreement with the experimental data that exists for cubane (C8H8). The trends among these molecules are reminiscent of those prevailing in the bulk solids of C, Si, and Ge. High-temperature dynamics and fragmentation of X8H8 were studied by the quantum molecular dynamics method which shows that at high temperatures cubane is transformed to the 8-fold ring structure of cyclooctotetraene.

We analyzed the dynamics of xenon atoms as lubricant between two Ni(110) slabs in relative motion. Atomic simulations are carried out by using classical molecular dynamics with realistic empirical potentials, where nickel as well as xenon atoms are relaxed. The resistance of the xenon layer against the loading force is examined and critical forces are determined to destroy the lubricant layer at different coverages. The relative motion of slabs in the lateral direction is investigated under constant normal force as a function of coverage ranging from zero to the monolayer xenon. Important lubrication properties of xenon atoms are analyzed by calculating the variation of potential energy, lateral force, and local hydrodynamic pressure. It is predicted that the corrugation of the potential energy associated with the sliding has a minimum value at submonolayer coverage. A phononic energy dissipation mechanism together with the theoretical analysis is proposed.

We have developed a microscopic model of phononic energy dissipation in friction that involves the generation of a local excess phonon distribution in a nanoparticle between two sliding objects, and its damping into the objects. The conversion of the energy stored in the nanoparticle into excess phonons and their decay rates are calculated. The model can be extended to include randomly distributed nanoparticles and phonon-phonon interaction through anharmonic couplings. By using this model we present a quantitative analysis of energy dissipation in sliding friction.

We investigate conductance through contacts created by pressing a hard tip, as used in scanning tunneling microscopy, against substrates. Two different substrates are considered, one a normal metal (Cu) and another a semi-metal (graphite). Our study involves the molecular dynamics simulations for the atomic structure during the growth of the contact, and selfconsistent field electronic structure calculations of deformed bodies. We develop a theory predicting the conductance variations as the tip approaches the surface. We offer an explanation for a quasiperiodic variation of conductance of the contact on the graphite surface, a behavior which is dramatically different from contacts on normal metals.

This paper presents an atomic-scale study of contact, indentation, and subsequent pulling and dry sliding of a sharp and blunt metal tip on a metal surface. The evolution of atomic structure and the variation of perpendicular and lateral forces are calculated by molecular-dynamics methods using an empirical potential based on the embedded-atom model. The sharp tip experiences multiple jumps to contact in the attractive force range. The contact interface grows discontinuously mainly due to disorder-order transformation leading to disappearance of a layer and hence abrupt changes in the normal-force variation. Atom exchange occurs in the repulsive range. During the pulling off, the connective neck is reduced discontinuously; however, not all the abrupt changes of the pulling force are associated with the creation of a new layer in the neck. The sliding of the sharp tip (or single asperity) induces two consecutive structural transformations that occur periodically, but end with the wear of a layer. The situation for a blunt tip is, however, quite different.

Simulations of dry sliding friction between a metal asperity and an incommensurate metal surface reveal unusual atomic processes. The lateral force exhibits a quasiperiodic variation with the displacement of an asperity; each period consists of two different stick-slip processes involving structural transitions. While one layer of asperity changes and matches the substrate lattice in the first slip, two asperity layers merge into a new one through a structural transition during the second slip. This leads to wear. The lateral force decreases abruptly during these slip stages, but it increases between two consecutive slips and resists the relative motion. The analysis of the order suggests that each structural transition is associated with a first-order phase transition. Nonadiabatic atomic rearrangements during these phase transitions involve a new kind of mechanism of energy dissipation in the dry sliding friction.

We present a theoretical study of dry sliding friction, which has a close bearing on the experiments done by using the atomic and friction force microscope. By performing atomic-scale calculations for the friction between a single atom and monoatomic infinite chain, we examined the effect of various material parameters on the stick-slip motion. We found that the perpendicular elastic deformation of the substrate that is induced by the sliding object is crucial for the energy damping in friction. In this case, the average friction force strongly depends on the perpendicular force constant of the substrate and the friction constant varies with the normal force. In particular, soft materials that continue to be elastic for a wide range of perpendicular compression may exhibit a second state. As a result, the hysteresis curve in the stick-slip motion becomes anisotropic.

In this paper we present an analysis of conduction through a single atom between two metal electrodes. Based on ab initio total-energy and electronic-structure calculations, and molecular-dynamics simulations using the embedded-atom model, we show that the conductance through an atom depends on the electronic structure of both the single atom and the metal electrodes, as well as the binding structure between the single atom and the surfaces of the metal electrodes. Our results enable us to interpret experimental results obtained by using a mechanical break junction on atomic-scale wires.

This paper presents a detailed analysis of atomic structure and force variations in metal nanowires under tensile strain. Our work is based on state of the art molecular dynamics simulations and ab initio self-consistent field calculations within the local density approximation, and predicts structural transformations. It is found that yielding and fracture mechanisms depend on the size, atomic arrangement, and temperature. The elongation under uniaxial stress is realized by consecutive quasielastic and yielding stages; the neck develops by the migration of atoms, but mainly by the sequential implementation of a new layer with a smaller cross section at certain ranges of uniaxial strain. This causes an abrupt decrease of the tensile force. Owing to the excessive strain at the neck, the original structure and atomic registry are modified; atoms show a tendency to rearrange in closed-packed structures. In certain circumstances, a bundle of atomic chains or a single atomic chain forms as a result of transition from the hollow site to the top site registry shortly before the break. The wire is represented by a linear combination of atomic pseudopotentials and the current is calculated to investigate the correlation between conductance variations and atomic rearrangements of the wire during the stretch. The origin of the observed "giant" yield strength is explained by using results of the present simulations and ab initio calculations of the total energy and Young's modulus for an infinite atomic chain.

We present the theoretical study of the controlled lateral and perpendicular motion of Xe on the Pt(111) surface. The lateral translation of Xe is manipulated by a tungsten tip of a scanning tunneling microscope. Using molecular statics and dynamics the energetics and different modes of atom translation are revealed. In the controlled and reversible transfer of Xe between two flat Pt(111) surfaces, effective charge on Xe, and the dipole moment of the Xe-Pt bond, are calculated as functions of the Xe-surface separation. The contributions of various mechanisms to the transfer rate of Xe are investigated by using the calculated quantum states of Xe under the applied bias voltage. These are tunneling and ballistic transfer, dipole excitation and excitation due to resonant tunneling of electrons, and electron wind force. We found that a single power law for the transfer rate does not exist in the whole range of applied pulse voltage. At high pulse voltage the transfer rate is dominated by the inelastic electron tunneling. At low pulse voltage the rate due to thermally assisted tunneling and ballistic transfer becomes important.

We show that an attractive interaction between two electrons confined to the surface of a sphere gives rise to a bound state, no matter how weak the interaction is. We explore the similarity between a sphere and a (two-dimensional) plane as far as pairing properties are concerned. We also discuss the relevance of the model to a recently discovered superconductor, alkali-metal-doped C60. © 1992 The American Physical Society.

The formation of the rectifying Schottky barrier on metal-semiconductor interfaces is one of the longest standing problems of solid-state physics. We present a review of the models and theories for Schottky barrier. Two important examples of metal-semiconductor interfaces, namely those containing simple and alkali metals, are analyzed in order to evaluate these models and theories in the light of ab-initio calculations. © 1991.

The authors have studied the electronic energy structure of pseudomorphic Gem/Sin superlattices by using the empirical tight-binding method. Effects of the band offset, sublattice periodicity and the lateral lattice constant on the transition energies have been investigated. They found that GemSin superlattices grown on Ge (001) can have a direct band gap, if m+n=10 and m=6. However, optical matrix elements for in-plane and perpendicular polarized light are negligible for the transition from the highest valence band to the lowest conduction band state at the centre of the superlattice Brillouin zone.

We present a comparative study of the pseudomorphic (Si)6/(Ge)6 and -doped (Si)3(Sb)(Si)2/(Ge)6 superlattices using the self-consistent pseudopotential method. The strained (Si)6/(Ge)6 superlattice has the lowest conduction-band states of extended character, and the difference of energy between the direct and indirect band gap is 70 meV. Upon doping by Sb in the Si sublattice, a quasi-two-dimensional band confined to the Sb layer dips into the band gap. Furthermore, the average potential in the Ge sublattice rises relative to that of the Si side, which increases the band offset, and enhances the localization of the quantum well states. These results indicate that doping provides new means for controlling the electronic properties of strained superlattices. © 1988 The American Physical Society.

A metallic carbon monolayer in the biphenylene network (specified as C ohs) becomes an insulator upon hydrogenation (specified as CH ohs). Patterned dehydrogenation of this CH ohs can offer a variety of intriguing functionalities. Composite structures constituted by alternating stripes of C and CH ohs with different repeat periodicity and chirality display topological properties and can form heterostructures with a tunable band-lineup or Schottky barrier height. Alternating arrangements of these stripes of finite size enable one to also construct double barrier resonant tunneling structures and 2D, lateral nanocapacitors with high gravimetric capacitance for an efficient energy storage device. By controlled removal of H atom from a specific site or dehydrogenation of an extended zone, one can achieve antidoping or construct 0D quantum structures like antidots, antirings/loops, and supercrystals, the energy level spacing of which can be controlled with their geometry and size for optoelectronic applications. Conversely, all these device functions can be acquired also by controlled hydrogenation of a bare C ohs monolayer. Since all these processes are applied to a monolayer, the commensurability of electronically different materials is assured. These features pertain not only to CH ohs but also to fully hydrogenated Si ohs.

When covered by gadolinium (Gd) atoms, silicene, a freestanding monolayer of Si atoms in a honeycomb network, remains stable above the room temperature and becomes a two-dimensional (2D) ferromagnetic semiconductor, despite the antiferromagnetic ground state of three-dimensional bulk GdSi2 crystal. In thin GdSi2 multilayers, even if magnetic moments are ordered parallel in the same Gd atomic planes, they are antiparallel between nearest Gd planes; hence they exhibit a ferrimagnetic behavior. In contrast, a freestanding Gd2Si2 monolayer constructed by covering silicene from both sides by Gd atoms is a stable antiferromagnetic metal due to the mirror symmetry. While multilayers covered by Gd from both sides having an odd number of Gd planes have a ferrimagneticlike ground state, even-numbered ones have antiferromagnetic ground state, but none of them is ferromagnetic. Silicon atoms intervening between Gd planes are responsible for these intriguing magnetic orders conforming with the recent experiments performed on Si(111) surface. Additionally, the magnetic states of these 2D gadolinium disilicide monolayers can be monitored by applied tensile strain and by the coverage/decoration of Gd. These predictions obtained by using first-principles, spin-polarized, density functional theory calculations combined with Monte Carlo simulations herald that C, B, Si, Ge, Sn, and their compounds functionalized by rare-earth atoms can lead to novel nanostructures in 2D spintronics.

Ciraci, Salim/0000-0001-8023-9860; Jahangirov, Seymur/0000-0002-0548-4820; Demirci, Salih/0000-0002-1272-9603 WOS:000516533300035 PubMed: 31970352 Semiconducting selenium and tellurium in their 3D bulk trigonal structures consist of parallel and weakly interacting helical chains of atoms and display a number of peculiarities. We predict that thermal excitations, 2D compressive strain and excess charge of positive and negative polarity mediate metal-insulator transitions by transforming these semiconductors into different metallic crystal structures. When heated to high temperature, or compressed, or charged positively, they change into a simple cubic structure with metallic bands, which is very rare among elemental crystals. When charged negatively, they transform first into body-centered tetragonal and subsequently into the body-centered orthorhombic structures with increasing negative charging. These two new structures stabilized by excess electrons also have overlapping metallic bands and quasi 2D and 1D substructures of lower dimensionality. Since the external charging of crystals can be achieved through their surfaces, the effects of charging on 2D structures of selenium and tellurium are also investigated. Similar structural transformations have been mediated also in 2D nanosheets and free-standing monolayers of these elements. These phase changes assisted by phonons are dynamical, reversible and tunable; the resulting metal-insulator transitions can occur within very short time intervals and may offer important device applications. Scientific and Technological Research Council of Turkey (TuBTAK)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [118F097]; National Center for High Performance Computing of Turkey (UHeM)Istanbul Technical University [5004132016]; TuBA, Turkish Academy of Sciences The Academy of Science of Turkey; The Academy of Science of Turkey - Outstanding Young Scientists Award Program (TuBA-GEBIP) This work was supported by the Scientific and Technological Research Council of Turkey (TuBTAK) under Project No 118F097. The computational resources are provided by TuBITAK ULAKBM, High Performance and Grid Computing Center (TR-Grid e-Infrastructure) and the National Center for High Performance Computing of Turkey (UHeM) under Grant No. 5004132016. S. D. thanks UNAM, National Nanotechnology Center at Bilkent University for the hospitality. S. C. thanks TuBA, Turkish Academy of Sciences The Academy of Science of Turkey for the financial Support. S. J. acknowledges support from The Academy of Science of Turkey - Outstanding Young Scientists Award Program (TuBA-GEBIP).

Despite its high solar absorbance and surface coating abilities, pristine graphene as a semimetal is not promising for photovoltaic applications. In this study, we predict that Glycine (Gly), an amino acid, which is normally bound to pristine graphene by a weak van der Waals attraction, can form an organic coating durable to ambient condition when adsorbed on vacancy patterned graphene surface. Moreover, adsorbed Gly coating induces metal-insulator transition and concomitantly increases the solar absorbance of pristine graphene more than three times. This way, graphene attain critical functionalities to be used in solar energy and photovoltaic applications.Despite its high solar absorbance and surface coating abilities, pristine graphene as a semimetal is not promising for photovoltaic applications. In this study, we predict that Glycine (Gly), an amino acid, which is normally bound to pristine graphene by a weak van der Waals attraction, can form an organic coating durable to ambient condition when adsorbed on vacancy patterned graphene surface. Moreover, adsorbed Gly coating induces metal-insulator transition and concomitantly increases the solar absorbance of pristine graphene more than three times. This way, graphene attain critical functionalities to be used in solar energy and photovoltaic applications.

This study unveils critical physical and chemical processes taking place at the interface between an amino acid, glycine, and defected graphene. Although glycine interacts weakly through van der Waals attraction with pristine graphene, it can set rather strong bonding at the close proximity of low-coordinated C atoms of single and triple vacancies and also at the edges of nanoribbons. The adsorption of a glycine molecule first leads to a reconstruction of the defect through a concerted process, which in turn induces magnetic metal-nonmagnetic insulator transition. This way, glycine can be pinned at the defect site with well-defined atomic configuration and electronic structure. In particular, libration frequency of the adsorbed glycine is attributed to significant restoring forces, which is essential for the self-assembly of glycines. Organic overlayer produced by self-assembled glycines on defect-patterned graphene constitutes a junction (heterostructure) with bilateral electronic and optical properties and offers novel device functions from biographene interfaces. These predictions are obtained from first-principles calculations using density functional theory. Authors acknowledges useful discussion with Dr. Urartu Şeker and Yelda Kadioglu. This research was supported in part by TÜBITAK̇ (The Scientific & Technological Research Council of Turkey) through TR-Grid e-Infrastructure Project, part of the calculations have been carried out at ULAKBIḾ computer center. S.C. acknowledges the financial support from the Academy of Science of Turkey TÜBA.

A suspended single layer of GaN in a honeycomb structure is stable in a planar geometry. By stacking these GaN layers one can construct bilayers or multilayers, even new three-dimensional (3D) periodic structures. In this study, we clarified how the planar layers are buckled with the onset of vertical Ga-N bonds. Among the four stable phases of bilayer GaN, only one of them maintains the planar geometry, which is bound by weak van der Waals interactions. For the remaining three phases, the layers are buckled with the onset of weak vertical bonds, and attain total energies slightly lower than that of the planar geometry. Structural phase changes, as well as direct-indirect band transitions take place under strain and electrostatic charging. The vertical bonds become shorter in multilayers, and eventually attain the bulk value. Among the stable phases of 3D periodic GaN, only one with a graphite-like structure behaves as a layered, van der Waals solid; whereby others are 3D uniform crystals beyond the van der Waals solid. The calculations were performed at TUBITAK ULAKBIM, High Performance and Grid Computing Center (TR-Grid e-Infrastructure) and the National Center for High Performance Computing of Turkey (UHeM) under grant no. 5003622015. This work was supported by the Scientific and Technological Research Council of Turkey (TUBITAK) under Project No. 117F241. E. D. acknowledges support from the Turkish Academy of Sciences - Outstanding Young Scientists Award Program (TUBA-GEBIP). S. C. acknowledges financial support from the Academy of Sciences of Turkey (TUBA).

Despite its strong N2 molecule, recent studies have shown that nitrogen, the lightest group V element, remains stable in the free-standing, single-layer buckled honeycomb structure with two-dimensional (2D) hexagonal lattice. This structure is called nitrogene and is predicted to be a nonmagnetic, wide band gap semiconductor or insulator. In this paper, we investigated the formation of a single vacancy, as well as the adsorption of selected single adatoms and molecules on 2D nitrogene, using the supercell method within the density functional theory. Through the consideration of large supercells, the couplings between adjacent vacancies and adspecies are minimized; hence, the results are taken to represent single, isolated defect and adspecies. We found that a single vacancy contributes a local magnetic moment and filled and empty localized gap states at low temperature but is prone to instability due to thermal excitations. Adatoms are bound to the surface of nitrogene and form localized gap states contributing a diversity of electronic and magnetic properties. Adsorption of adatoms, such as B, C, Si, and N, however, give rise to local and strong reconstruction in nitrogene in their close proximity. Notably, a N adatom forms a strong N2 molecule by removing one N atom from nitrogene and leaves a vacancy behind. Conversely, the interactions between selected molecules, such as H2, O2, H2O, and N2, and the surface of nitrogene are rather weak and do not induce any change in the physical properties. However, H2 and O2 can be dissociated at the edges of a nitrogene flake and concomitantly can remove host N atoms to form NH2 and NO2 molecules. Calculated properties of adatoms adsorbed to nitrogene differ dramatically from the properties of those adsorbed to single-layer structures of other group V elements.

Bu tez düz, bağımsız tek tabaka kare-sekizgen (so) GaN ve AlN yapılarhakkındadır. Yoğunluk fonksiyonu teorisi (YFT) kullanılarak tek tabaka veçoklu tabakalı so-GaN ve so-AlN yapıların, kararlılıkları, elektronik özelliklerive fonksiyonelleştirilmeleri; adsorbe atomlar ve atomik boşluklar, temel prensiplerpseudo potansiyel düzlem dalga hesapları kullanarak inceledik. Dinamikve termal kararlıkların kapsamlı bir analizini, temel prensipler sonlu sıcaklıkmoleküler dinamiği ve kızıl ötesi Raman aktif modların birlikte analiz edildiğifonon hesaplarına göre yaptık. Bu GaN ve AlN'ın tek katmanlı kare-sekizgenyapıları, yöne bağımlı mekanik özellikler gösterir ve altıgen emsallerine kıyasladaha küçük, temel dolaylı bant aralıklarına sahipler. Bu YFT band aralıkları,düzeltmelerle artabilirler ve daha da geniş olabilirler de. Tek doğrultuda ve çiftdoğrultuda çekme deformasyonları altında temel band aralıkları azalır ve kapanabilirler.Tek katmanların üst üste yığılmasıyla oluşturulan çift katmanlı, üç katmanlı ve üç boyutlu (3B) katmanlı yapıların enerjetikleri, bağlanmaları ve sonuçta oluşan elektronik yapıları incelendi. van der Waals yapılarına kıyasla, katmanlar arasında bariz bir kimyasal bağ kurulması, bağlanmayı etkiler ve bükülmelere neden olarak düzlemsel geometriyi değiştirir. Yığılma dizilenmesineve geometrisine bağlı olarak, enerjetikleri, zayıf dikey bağların sayısı ve direkt band aralıklı elektronik yapıları, ayarlanabilir geniş bir çeşitlilik umudu vaad eden ilgi çekici varyasyonlar gösterir. Ayrıca, tek katmanlı yapıların elektronik ve manyetik özellikleri, çeşitli atomların adsorpsiyonu ya da nötr katyon-anyon boşluğu yaratılarak modifiye edilebilir. Tek tabaka so-GaN ve so-AlN yapılarının düz ve dikey heteroyapıları, gelecek çalışmaları olarak düşünülebilirler. This thesis, deals with the planar free-standing, single-layer, square-octagon (SO)structures of GaN and AlN. We investigated single-layer and multilayer so-GaNand so-AlN structures, their stability, electronic properties and functionalization;adatom and vacancies using first principles pseudopotential plane wave calculations.We performed an extensive analysis of dynamical and thermal stabilityin terms of ab-initio finite temperature molecular dynamics and phonon calculationstogether with the analysis of Raman and infrared active modes. Thesesingle layer square-octagon structures of GaN and AlN display directional mechanicalproperties, and have fundamental indirect band gaps, which are smallerthan their hexagonal counter parts. These DFT band gaps, however, increaseand become wider upon correction. Under uniaxial and biaxial tensile strainthe fundamental band gaps decrease and can be closed. The energetics, bindingand resulting electronic structure of bilayer, trilayer and 3D layered structuresconstructed by stacking of the single layers were examined. In contrast to thevan der Waals solids, a signicant chemical bonding between layers affects thebinding and transforms the planar geometry by inducing buckling. Depending onthe stacking sequence and geometry, energetics, number of weak vertical bondsand direct band gap electronic structure display interesting variations promisinga wide range of tunability. Furthermore, electronic and magnetic properties ofthese single-layer structures can be modied by adsorption of various adatoms,or by creating neutral cation-anion vacancies. As a future work, in-plane andvertical heterostructures of single layer so-GaN and so-AlN structures could beconsidered. 82

Akturk, Ethem/0000-0002-1615-7841; Demirci, Salih/0000-0002-1272-9603 WOS: 000418655400016 This paper reveals how the electronic structure, magnetic structure, and topological phase of two-dimensional (2D), single-layer structures of bismuth are modified by point defects. We first showed that a free-standing, single-layer, hexagonal structure of bismuth, named h-bismuthene, exhibits nontrivial band topology. We then investigated interactions between single foreign adatoms and bismuthene structures, which comprise stability, bonding, electronic structure, and magnetic structures. Localized states in diverse locations of the band gap and resonant states in band continua of bismuthene are induced upon the adsorption of different adatoms, which modify electronic and magnetic properties. Specific adatoms result in reconstruction around the adsorption site. Single vacancies and divacancies can form readily in bismuthene structures and remain stable at high temperatures. Through rebondings, Stone-Whales-type defects are constructed by divacancies, which transform into a large hole at high temperature. Like adsorbed adatoms, vacancies induce also localized gap states, which can be eliminated through rebondings in divacancies. We also showed that not only the optical and magnetic properties, but also the topological features of pristine h-bismuthene can be modified by point defects. The modification of the topological features depends on the energies of localized states and also on the strength of coupling between point defects. TUBA, Turkish Academy of Sciences (Turkey); Research Fund of Adnan Menderes University (Turkey) [MF-16004] The computational resources are provided by TUBITAK ULAKBIM, High Performance and Grid Computing Center (TR-Grid e-Infrastructure). S.C. acknowledge financial support from TUBA, Turkish Academy of Sciences (Turkey). This research was supported by Research Fund of Adnan Menderes University (Turkey), Project No. MF-16004. We thank Dominik Gresch for helpful discussions on operating Z2-PACK.

Based on first-principles phonon and finite temperature molecular dynamics calculations including spin-orbit coupling, we showed that free-standing single-layer phases of bismuth, namely buckled honeycomb and asymmetric washboard structures named as bismuthene, are stable at high temperature. We studied the atomic structure, mechanical, and electronic properties of these single-layer bismuthene phases and their bilayers. The spin-orbit coupling is found to be crucial in determining lattice constants, phonon frequencies, band gaps, and cohesion. In particular, phonons of 3D hexagonal crystal, as well as those of single-layer bismuthene phases, are softened with spin orbit coupling. By going from 3D hexagonal crystal to free-standing single-layer structures, 2D hexagonal lattice is compressed and semimetal is transformed to semiconductor as a result of confinement effect. On the contrary, by going from single-layer to bilayer bismuthenes, the lattice is slightly expanded and fundamental band gaps are narrowed. Our results reveals that interlayer coupling in multilayer and 3D Bi crystal is crucial for topologically trivial to nontrivial and semimetal to semiconductor transitions.

Bu tez çalışması, çeşitli yeni iki boyutlu balpeteği yapıların elektronik, manyetik, mekanik ve optik özelliklerini ortaya koyarak bu yapıların nano ölçekte yeni cihaz tasarımı için kullanılabilirliklerinin yoğunluk fonksiyoneli teorisi ile incelenmesini kapsamaktadır. Ayrıca, kuantum mekaniksel moleküler dinamik simülasyonları ve fonon analizleri yardımıyla yeni iki boyutlu malzeme öngörüleri ve mevcut iki boyutlu malzemelerin muhtemel yeni kararlı fazları detaylı olarak incelenmiştir.İlk olarak, yoğunluk fonksiyoneli teorisiyle geliştirilen hesaplama yöntemleriyle iki boyutlu grafen ve boron nitrat kompozit malzemeleri incelenerek, dikey ve yatay grafen / boron nitrat kompozitlerinin büyüme adımları gösterilmiştir. Daha sonra, bu kompozit malzemelere dışardan elektrik alan uygulanarak, bu sistemlerde depolanan enerji ve elektriksel yük değerleri hesaplanmıştır. Dolayısıyla, grafen / boron nitrat kompozit malzemelerin yüksek performaslı nanokapasitör olarak kullanılabiliecekleri gösterilmiştir. Bu nanokapasitörler, geniş boyutlarda klasik kapasitörler gibi davranmalarına karşın, boyutları nano ölçeğe indirilidiğinde kuantum mekaniksel davranışlar sergilemektedirler. Tezin daha sonraki bölümünde, düzlemsel olarak büyütülen grafen / boron nitrat kompozit malzemelerinin çeşitli özelliklerinin, kompozit içinde bulunan grafen veya boron nitrat miktarına göre nasıl değiştiği incelenmiştir. Farklı kombinasyonlar kullanılarak alaşımlar, çizgisel kompozitler ve ince katkılama tarzı malzemeler elde edilerek bunların atom inceliğinde devrelerde kullanım için özellikleri hesaplanmıştır.Ayrıca, karbon / boron nitrat nano kompozitlerinin kısa atomik zinciler şeklinde büyümeleri incenerek, bu zincirlerin yüksek sıcaklıklarda bozulmadan kararlı olarak kalabildikleri gösterilmiştir. Zincirlerin elektronik ve manyetik özelliklerinin zincirdeki atom sayısına göre çift / tek disparitesi gösterdiği gözlemlenmiştir. Ayrıca, bu zincirlerin düzlemsel olarak birleştirilmesi sonucu elde edilen ve yeni bir iki boyutlu malzeme olan alfa-grafen yapısının kararlılığı fonon analizleriyle ispatlanmıştır.Tezin son iki bölümünde grafenin silikon, germanyum, azot ve antimon benzerleri incelenmiştir. İki boyutlu silikon ve germanyum yapılarında oluşan kafes tarzı yeni geometrik yapılar ortaya konularak, bu kafes yapısının tabakalı silikon ve germanyum elde edilmesinde temel unsur olduğu gösterilmiştir. Tezin son bölümünde, yeni malzeme tasarımı ve öngörüleri üzerinde durularak, iki boyutlu silika, iki boyutlu azot ve antimon bal peteği benzeri yapılarının kararlı geometrileri ve bu yapıların özellikleri açıklanmıştır. This thesis presents a variety of new two dimensional honeycomb-like structures and heterostructures; the main objective being to determine their fundamental electronic, magnetic, mechanical and optical properties for new device and material design. Utilization of existing two dimensional materials for nanoscale device design, understanding the fundamental properties of their composite structures, explaining the existing data on known two dimensional materials and using computational simulations to discover new materials are the main concerns of this thesis.We begin by assessing the validity of density functional theory on monolayer composites of graphene and boron nitride. We show that it is possible to grow vertical graphene / boron nitride heterostructures on top of each other and reveal the growth mechanisms at the atomistic level. We then utilize this vertical heterostructure for a nanoscale capacitor design by applying an external electric field. We test and show how first principles methods can be used to investigate the properties of materials under electric field. After explaining the reliable methods, capacitance values are calculated for the model for various thicknesses, which show quantum mechanical size effects at small separations that recede as the separations get larger; as the later is confirmed by experimental observations.The next part of the thesis, investigates the electronic properties of lateral graphene / boron nitride heterostructures, and show how these composites act differently depending on the concentrations of graphene and boron nitride in the composite system. Namely, different behaviors of alloys, $/delta$-doping and line compounds are revealed. Following this, these lateral heterostructures are utilized as nanoscale planar capacitors for atomically thin circuitry.As a final remark on carbon and boron nitride nanocomposites, the next chapter of this thesis describes the growth mechanisms of one dimensional carbon/boron nitride short atomic chains and show their stabilities at elevated temperatures. The electronic and magnetic properties of these chains exhibit even/odd disparity depending on the number of atoms in the chain. These chains also construct another two dimensional allotrope of graphene, namely graphyne, when connected to each other on the same plane. The properties of graphyne and its boron nitride analogue described in the following chapter introduces a new monolayer allotrope of carbon and boron nitride.The following chapter turns to silicon and germanium analogue of graphene, silicene and germanene. Dumbbell type reconstructions of silicene and germanene are introduced, which lead to layered silicene and germanene. Dumbbell units introduced here form the fundamental building blocks of experimentally observed layered silicene and germanene.The last chapter of the thesis looks at new material design and prediction studies based on computational simulations. Oxygenated silicene leads to a new monolayer piezoelectric material called silicatene. Finally, the monolayer structures of Group V elements nitrogen and antimony are also shown to be stable by phonon calculations and high temperature molecular dynamics simulations. 195

We study the interaction of H$_2$, O$_2$, CO, H$_2$O and OH molecules with the vacancy defects of graphene and silicene. Atoms around the bare vacancy reconstruct and specific chemically active sites are created. While H$_2$, O$_2$ and CO remain intact on both pristine graphene and silicene, these molecules can dissociate when they are placed at the close proximity of these chemically active sites and nucleate centers for the hydrogenation and oxygenation. Saturation of the dangling bonds at the defect sites by constituent atoms of dissociated molecules gives rise to significant modification of electronic and magnetic properties. We analyzed the mechanism of the dissociation and revealed a concerted action of surrounding host atoms together with dissociated molecules to lower the energy barrier needed for dissociation. The dissociations of H$_2$O and OH are hindered by high energy barriers. Our study suggests that graphene and silicene can be functionalized by creating meshes of single vacancy, where specific molecules can dissociate, while some other molecules can be pinned., Published in J. Phys. Chem. C

Cataloged from PDF version of article. Single-layer core-shell structures consisting of graphene as the core and hexagonal boron nitride as the shell are studied using the first-principles plane-wave method within density functional theory. Electronic energy level structure is analyzed as a function of the size of both core and shell. It is found that the confinement of electrons in a two-dimensional graphene quantum dot is reduced by the presence of a boron nitride shell. The energy gap is determined by the graphene states. Comparison of round, hexagonal, rectangular, and triangular core-shell structures reveals that their electronic and magnetic states are strongly affected by their geometrical shapes. The energy level structure, energy gap, and magnetic states can be modified by external charging. The core part acts as a two-dimensional quantum dot for both electrons and holes. The of extra electron intake capacity of these quantum dots is shown to be limited by the Coulomb blockade in two dimensions.

Germanene, a graphene like single layer structure of Ge, has been shown to be stable and recently grown on Pt and Au substrates. We show that a Ge adatom adsorbed to germanene pushes down the host Ge atom underneath and forms a dumbbell structure. This exothermic process occurs spontaneously. The attractive dumbbell-dumbbell interaction favors high coverage of dumbbells. This letter heralds stable new phases of germanene, which are constructed from periodically repeating coverage of dumbbell structures and display diversity of electronic and magnetic properties., Published in JPCL http://pubs.acs.org/doi/abs/10.1021/jz500977v

Based on first-principles calculations, we predict two new thermodynamically stable layered-phases of silicon, named as silicites, which exhibit strong directionality in the electronic and structural properties. As compared to silicon crystal, they have wider indirect band gaps but also increased absorption in the visible range making them more interesting for photovoltaic applications. These stable phases consist of intriguing stacking of dumbbell patterned silicene layers having trigonal structure with √3×√3 periodicity of silicene and have cohesive energies smaller but comparable to that of the cubic diamond silicon. Our findings also provide atomic scale mechanisms for the growth of multilayer silicene as well as silicites., S.C. and V.O.Ö acknowledge financial support from the Academy of Sciences of Turkey (TUBA). S. Cahangirov and A. Rubio acknowledges financial support from the Marie Curie grant FP7-PEOPLE-2013-IEF Project No. 628876, the European Research Council (ERC-2010-AdG-267374), Spanish grant (FIS2010-21282-C02-01), Grupos Consolidados(IT578-13), and the EU project (280879-2 CRONOS CP-FP7).

Silica or SiO2, the main constituent of Earth’s rocks has several 3D complex crystalline and amorphous phases, but it does not have a graphitelike layered structure in 3D. Our theoretical analysis and numerical calculations from the first principles predict a single-layer honeycomblike allotrope, hα silica, which can be viewed to be derived from the oxidation of silicene and it has intriguing atomic structure with reentrant bond angles in hexagons. It is a wide band gap semiconductor, which attains remarkable electromechanical properties showing geometrical changes under an external electric field. In particular, it is an auxetic metamaterial with a negative Poisson’s ratio and has a high piezoelectric coefficient. While it can form stable bilayer and multilayer structures, its nanoribbons can show metallic or semiconducting behavior depending on their chirality. Coverage of dangling Si orbitals by foreign adatoms can attribute new functionalities to hα silica. In particular, Si2O5, where Si atoms are saturated by oxygen atoms from top and bottom sides alternatingly can undergo a structural transformation to make silicatene, another stable, single layer structure of silica., This work was partially supported by the Academy of Sciences of Turkey (TUBA). S. Cahangirov acknowledges Marie Curie Grant No. FP7-PEOPLE-2013-IEF, project ID 628876, and Grupos Consolidados UPV/EHU del Gobierno Vasco (Grant No. IT578-13).

We present a first-principles study of various effects of charging and electric field on the oxidation/deoxidation of graphene oxide consisting of only epoxy groups. We first determined the proper basis set, which hinders the spurious spilling of electrons of graphene oxide when negatively charged or exerted by perpendicular electric field, and treated with periodic boundary conditions. We then showed that the electric field perpendicularly applied to graphene surface provide side-specific functionalization. We found that the bonds between oxygen and graphene are weakened under applied electric field. For specific values of excess charge or electric field, an oxygen atom that is normally adsorbed to the bridge site in equilibrium moves to the top site. By directly charging and/or by applying electric field, one can monitor this migration as well as desorption of the oxygen adatom. In spite of the negative formation energy, an energy barrier prevents individually adsorbed oxygen atoms from forming oxygen molecules. This energy barrier is dramatically weakened upon negative charging or exertion of an electric field. Our results explain why the reduction of graphene oxide can be facilitated by these external effects. © 2013 American Chemical Society.

Titanium atoms are adsorbed to graphene with a significant binding energy and render diverse functionalities to it. Carrying out first-principles calculations, we investigated the effects of charging and static electric field on the physical and chemical properties of graphene covered by Ti adatoms. When uniformly Ti covered graphene is charged positively, its antiferromagnetic ground state changes to ferromagnetic metal and attains a permanent magnetic moment. Static electric field applied perpendicularly causes charge transfer between Ti and graphene, and can induce metal-insulator transition. While each Ti adatom adsorbed to graphene atom can hold four hydrogen molecules with a weak binding, these molecules can be released by charging or applying electric field perpendicularly. Hence, it is demonstrated that charging and applied static electric field induce quasi-continuous and side specific modifications in the charge distribution and potential energy of adatoms absorbed to single-layer nanostructures, resulting in fundamentally crucial effects on their physical and chemical properties. © 2013 IOP Publishing Ltd.

We investigate a nanoscale dielectric capacitor model consisting of two-dimensional, hexagonal h-BN layers placed between two commensurate and metallic graphene layers using self-consistent field density functional theory. The separation of equal amounts of electric charge of different sign in different graphene layers is achieved by applying electric field perpendicular to the layers. The stored charge, energy, and the electric potential difference generated between the metallic layers are calculated from the first-principles for the relaxed structures. Predicted high-capacitance values exhibit the characteristics of supercapacitors. The capacitive behavior of the present nanoscale model is compared with that of the classical Helmholtz model, which reveals crucial quantum size effects at small separations, which in turn recede as the separation between metallic planes increases., Published version in The Journal of Physical Chemistry: http://pubs.acs.org/doi/abs/10.1021/jp403706e

Bu tezde ilk prensiplere dayanarak bal peteği örgüsüne sahip iki boyutlu nano yapıların üzerine elektriksel yüklenmenin etkilerini günümüz gelişmiş metodlarını kullanarak inceledik. Grafen, molibden disülfür (MoS2), bor nitrür (BN), grafan (CH), ve folorografen (CF) yakın zamanda sentezlenebildi ve çok önemli yapısal, elektriksel ve manyetik özelliklere sahiptirler. Bu bağlamda bize göre bu malzemelerin elektriksel yük altında fiziksel özelliklerinin değişiminin incelenmesi ileriki olası uygulamalar ve bu malzemelerin daha iyi anlaşılabilmesi için önem arz etmektedir.Yapıdan elektron çekilmesiyle bağ uzunluklarının ve dolayısıyla örgü vektörlerinin büyüdüğünü gösterdik. Bu sebepten fononlar yumuşadı ve Raman-aktif fonon modlarının frekansları düştü. Normalde oldukça yüksek yasak enerji aralığına sahip olan BN ve MoS2 gibi malzemeler iletken haline geldiler. Pozitif yüklenme neticesinde artı yüklerin bu malzemelerin üç katmanlı yapılarında en dış katmanlarında toplandığı görüldü. Daha sonrasında pozitif yüklenme miktarını arttırılmasıyla birbirlerine zayıf van der Waals bağlarıyla bağlanmış olan katmanların ayrıldığı görüldü. Bu neticeler elektriksel yüklenme yardımıyla çok katmanlı grafit, BN ve MoS2 yapılarından tekli katmanların elde edilebilmesini öngörmektedir. Ek olarak bazı atomların elektriksel yüklenme neticesinde grafen üzerine bağlanma enerjilerinin ve manyetik momentlerinin değiştirilebileceğini gösterdik. Düzlem dalga metodunun sınır koşulları içinde kullanılmasıyla ortaya çıkan yapay yetersizliklerin atomik orbital tabanlı başka yöntemler kullanılarak aşılabileceğini gösterdik.Oksitlenmiş grafen üzerine elektriksel yükün etkilerini araştırmaya başlamadan önce oksijen atomlarının grafen üzerine bağlanmasını detaylı birşekilde inceledik. Grafen bağları üzerindeki elektriksel yük miktarının oksijen atomlarının grafen üzerine bağlanmasını kontrol eden en önemli unsur olduğunu ortaya çıkardık. Daha sonrasında ise oksijen atomlarının grafen üzerindeki difüzyon bariyerlerinin elektriksel yüklenme ile belirgin şekilde değiştiğini gösterdik. Elde ettiğimiz bu sonuçlar deneysel verilerdeki pozitif yüklenmenin grafenin oksitlenmesine yol açtığını negatif yüklenmenin ise oksitlenmiş grafenin normal grafene dönüşmesine yol açtığı şeklindeki sonuçlarını kısmen desteklemektedir ve başka etkenlerin de bu oluşumlarda rol oynayabileceğini öngörmektedir. In this thesis we employ state-of-the-art ? rst-principles calculations based on density functional theory (DFT) to investigate the e ? ects of static charging on two-dimensional (2D) honeycomb nanostructures. Free standing, single-layer graphene and other similar single-layer honeycomb structures such as boron nitride (BN), molybenum disul ? de (MoS2 ), graphane (CH) and ? uorographene (CF) have been recently synthesized with their unusual structural, electronic and magnetic properties. Through understanding of the e ? ects of charging on these nanostructures is essential from our points of view in order to better understand their fundamental physics and developing useful applications.We show that the bond lengths and hence 2D lattice constants increase asa result of electron removal from the single layer. Consequently, phonons soften and the frequencies of Raman active modes are lowered. Three-layer, wide band gap BN and MoS2 sheets are metalized while these slabs are wide band semiconductors, and excess positive charge is accumulated mainly at the outermost atomic layers. Excess charges accumulated on the surfaces of slabs induce repulsive force between outermost layers. With increasing positive charging the spacing between these layers increases, which eventually ends up with exfoliation when exceeded the weak van der Waals (vdW) attractions between layers. Thisresult may be exploited to develop a method for intact exfoliation of graphene, BN and MoS2 multilayers. In addition we also show that the binding energy and local magnetic moments of speci ? c adatoms can be tuned by charging. We have addressed the de ? ciencies that can occur as an artifact of using plane-wave basis sets in periodic boundary conditions and proposed advantages of using atomic orbital based methods to overcome these de ? ciencies. Using the methods and computation elucidated in this thesis, the e ? ects of charging on periodic as wellas ? nite systems and the related properties can now be treated with reasonable accuracy.The adsorption of oxygen atoms on graphene have been investigated exten-sively before dealing with the charging of graphene oxide (GOX). The energetics and the patterns of oxygen coverage trends are shown to be directly related with the amount of bond charge at the bridge sites of graphene structure. We ? nally showed that the di ? usion barriers for an oxygen atom to migrate on graphene surface is signi ? cantly modi ? ed with charging. While the present results comply with the trends observed in the experimental studies under charging, we believe that there are other factors a ? ecting the reversible oxidation-reduction processes. 108

We perform first-principles structure optimization, phonon frequency and finite temperature molecular dynamics calculations based on density functional theory to study the interaction of chlorine atoms with graphene predicting the existence of possible chlorinated graphene derivatives. The bonding of a single chlorine atom is ionic through the transfer of charge from graphene to chlorine adatom and induces negligible local distortion in the underlying planar graphene. Different from hydrogen and fluorine adatoms, the migration of a single chlorine adatom on the surface of perfect graphene takes place almost without barrier. However, the decoration of one surface of graphene with Cl adatoms leading to various conformations cannot sustain due to strong Cl-Cl interaction resulting in the desorption through the formation of Cl$_2$ molecules. On the contrary, the fully chlorinated graphene, chlorographene CCl, where single chlorine atoms are bonded alternatingly to each carbon atom from different sides of graphene with $sp^3$-type covalent bonds, is buckled. We found that this structure is stable and is a direct band gap semiconductor, whose band gap can be tuned by applied uniform strain. Calculated phonon dispersion relation and four Raman-active modes of chlorographene are discussed., Comment: http://pubs.acs.org/doi/abs/10.1021/jp307006c

Nucleation and growth mechanisms of short chains of carbon atoms on single-layer, hexagonal boron nitride (h-BN), and short BN chains on graphene are investigated using first-principles plane wave calculations. Our analysis starts with the adsorption of a single carbon ad-atom and examines its migrations. Once a C$_2$ nucleates on h-BN, the insertion of each additional carbon at its close proximity causes a short segment of carbon atomic chain to grow by one atom at at a time in a quaint way: The existing chain leaves its initial position and subsequently is attached from its bottom end to the top of the carbon ad-atom. The electronic, magnetic and structural properties of these chains vertically adsorbed to h-BN depend on the number of carbon atoms in the chain, such that they exhibit an even-odd disparity. An individual carbon chain can also modify the electronic structure with localized states in the wide band gap of h-BN. As a reverse situation we examined the growth of short BN atomic chains on graphene, which attribute diverse properties depending on whether B or N is the atom bound to the substrate. These results together with ab-initio molecular dynamics simulations of the growth process reveal the interesting self-assembly behavior of the grown chains. Furthermore, we find that these atomic chains enhance the chemical activity of h-BN and graphene sheets by creating active sites for the bonding of various ad-atoms and can act as pillars between two and multiple sheets of these honeycomb structures leaving wider spacing between them to achieve high capacity storage of specific molecules., Accepted for Physical Review B