Plane-wave Density Functional Theory Calculations Research Articles

Structure and energetics of extended defects in ice Ih

We consider the molecular structure and energetics of extended defects in proton-disordered hexagonal ice I${}_{h}$. Using plane-wave density functional theory (DFT) calculations, we compute the energetics of stacking faults and determine the structure of the ${30}^{\ensuremath{\circ}}$ and ${90}^{\ensuremath{\circ}}$ partial dislocations on the basal plane. Consistent with experimental data, the formation energies of all fully reconstructed stacking faults are found to be very low. This is consistent with the idea that basal-plane glide dislocations in ice I${}_{h}$ are dissociated into partial dislocations separated by an area of stacking fault. For both types of partial dislocation we find a strong tendency toward core reconstruction through pairwise hydrogen-bond reformation. In the case of the ${30}^{\ensuremath{\circ}}$ dislocation, the pairwise hydrogen-bond formation leads to a period-doubling core structure equivalent to that seen in zinc-blende semiconductor crystals. For the ${90}^{\ensuremath{\circ}}$ partial we consider two possible core reconstructions, one in which the periodicity of the structure along the core remains unaltered and another in which it is doubled. The latter is preferred, although the energy difference between both is rather small, so that a coexistence of both reconstructions appears plausible. Our results imply that a mobility theory for dislocations on the basal plane in ice I${}_{h}$ should be based on the idea of reconstructed partial dislocations.

Computational study of ethanol adsorption and reaction over rutile TiO2 (110) surfaces

Studies of the modes of adsorption and the associated changes in electronic structures of renewable organic compounds are needed in order to understand the fundamentals behind surface reactions of catalysts for future energies. Using planewave density functional theory (DFT) calculations, the adsorption of ethanol on perfect and O-defected TiO(2) rutile (110) surfaces was examined. On both surfaces the dissociative adsorption mode on five-fold coordinated Ti cations (Ti(4+)(5c)) was found to be more favourable than the molecular adsorption mode. On the stoichiometric surface E(ads) was found to be equal to 0.85 eV for the ethoxide mode and equal to 0.76 eV for the molecular mode. These energies slightly increased when adsorption occurred on the Ti(4+)(5c) closest to the O-defected site. However, both considerably increased when adsorption occurred at the removed bridging surface O; interacting with Ti(3+) cations. In this case the dissociative adsorption becomes strongly favoured (E(ads) = 1.28 eV for molecular adsorption and 2.27 eV for dissociative adsorption). Geometry and electronic structures of adsorbed ethanol were analysed in detail on the stoichiometric surface. Ethanol does not undergo major changes in its structure upon adsorption with its C-O bond rotating nearly freely on the surface. Bonding to surface Ti atoms is a σ type transfer from the O2p of the ethanol-ethoxide species. Both ethanol and ethoxide present potential hole traps on O lone pairs. Charge density and work function analyses also suggest charge transfer from the adsorbate to the surface, in which the dissociative adsorptions show a larger charge transfer than the molecular adsorption mode.

Theoretical studies of adsorption property on Ir 4/MgO and Ir 4/γ-Al 2O 3

The adsorption properties of atomic and molecular species on Ir 4/MgO and Ir 4/γ-Al 2O 3 have been systematically studied by means of planewave density functional theory (DFT) calculations using the periodic boundary conditions. The binding energies of these species were ordered as follows: H 2O<C 2H 4<H<OH<S< N<O<C. The adsorption energies of adatoms on Ir 4/MgO were larger than those on Ir 4/γ-Al 2O 3 except hydrogen atom, but were in reverse for the molecules calculated. In addition, the difference of adsorption energies on MgO and γ-Al 2O 3 supports has been elucidated by analyzing the electronic properties. A detailed investigation on state density clarifies the nature of the magnitude of adsorption energy. These calculated results are consistent well with the available experimental and theoretical results.

The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT Calculations.

The adsorption of Ag, Au, and Pd atoms on benzene, coronene, and graphene has been studied using post Hartree–Fock wave function theory (CCSD(T), MP2) and density functional theory (M06-2X, DFT-D3, PBE, vdW-DF) methods. The CCSD(T) benchmark binding energies for benzene–M (M = Pd, Au, Ag) complexes are 19.7, 4.2, and 2.3 kcal/mol, respectively. We found that the nature of binding of the three metals is different: While silver binds predominantly through dispersion interactions, the binding of palladium has a covalent character, and the binding of gold involves a subtle combination of charge transfer and dispersion interactions as well as relativistic effects. We demonstrate that the CCSD(T) benchmark binding energies for benzene–M complexes can be reproduced in plane-wave density functional theory calculations by including a fraction of the exact exchange and a nonempirical van der Waals correction (EE+vdW). Applying the EE+vdW method, we obtained binding energies for the graphene–M (M = Pd, Au, Ag) complexes of 17.4, 5.6, and 4.3 kcal/mol, respectively. The trends in binding energies found for the benzene–M complexes correspond to those in coronene and graphene complexes. DFT methods that use empirical corrections to account for the effects of vdW interactions significantly overestimate binding energies in some of the studied systems.

Density functional study of TaSin (n = 1–3, 12) clusters adsorbed to graphene surface

A plane-wave density functional theory (DFT) calculations have been performed to investigate structural and electronic properties of TaSin (n=1–3, 12) clusters supported by graphene surface. The resulting adsorption structures are described and discussed in terms of stability, bonding, and electron transfer between the cluster and the graphene. The TaSin clusters on graphene surface favor their free-standing ground-state structures. Especially in the cases of the linear TaSi2 and the planar TaSi3, the graphene surface may catalyze the transition of the TaSin clusters from an isomer of lower dimensionality into the ground-state structure. The adsorption site and configuration of TaSin on graphene surface are dominated by the interaction between Ta atom and graphene. Ta atom prefers to adsorb on the hollow site of graphene, and Si atoms tend to locate on the bridge site. Further, the electron transfer is found to proceed from the cluster to the surface for n=1 and 2, while its direction reverses as n>2. For the case of TaSi, chemisorption is shown to prevail over physisorption as the dominant mode of surface–adsorbate interaction by charge density analysis.

Molecular-Scale Structure of a Nitrobenzene Monolayer on Si(001)

Nitrobenzene molecules can be attached to Si-(001) by exposing the Si(001) (2 × 1) surface to nitrobenzene gas at room temperature. The resulting monolayer lacks long-range order in scanning tunneling microscopy images but shows signs of a local periodic arrangement of molecules. Self-consistent plane-wave density functional theory calculations find that the energy gained per molecule in the adsorption of nitrobenzene is nearly constant as a function of nitrobenzene coverage and that it is energetically favorable to form coverages as high as one molecule per Si dimer. Ab initio molecular dynamics (AIMD) simulations show that the migration of oxygen transforms an initial configuration in which the nitrobenzene molecule bridges a Si dimer into lower energy configurations with oxygen separated from the nitrobenzene phenyl group. A previously unknown low-energy configuration, characteristic of SiO2 bonding, is identified by the AIMD calculations. The energy barriers for O migration into Si backbonds are calculated by using the climbing-image nudged elastic band method. The calculated dipole moments of nitrobenzene on Si(001) varied from 0.11 to 0.45 D, depending on the molecular configuration. Nitrogen is observed using X-ray photoelectron spectroscopy in a concentration consistent with the attachment of one nitrobenzene molecule per Si dimer.

Minerals from Macedonia. XXVII: Theoretical and experimental study of the vibrational spectra of endemic nežilovite

Endemic mineral nežilovite was studied by vibrational spectroscopy (IR and Raman), quantum theoretical methods and X-ray powder diffraction. Experimental Raman as well as the higher-frequency region of the infrared spectra of this mineral closely resembles to the corresponding spectra of magnetoplumbite-group minerals, while the appearance of the lower-frequency part of the IR spectra is markedly similar to the corresponding region in Ba-ferrite. Essentially, all bands in the experimental spectra were tentatively assigned. In most cases, the assignments were either supported or implied by the theoretical data obtained on the basis of plane-wave pseudopotential density functional theory (DFT) calculations.

Initial steps in methanol steam reforming on PdZn and ZnO surfaces: Density functional theory studies

Recent experiments suggested that PdZn alloy on ZnO support is a very active and selective catalyst for methanol steam reforming (MSR). To gain insight into MSR mechanism on this catalyst, plane-wave density functional theory calculations were carried out on the initial steps of MSR on both PdZn and ZnO surfaces. Our calculations indicate that the dissociation of both methanol and water is highly activated on flat surfaces of PdZn such as (111) and (100), while the dissociation barriers can be lowered significantly by surface defects, represented here by the (221), (110), and (321) faces of PdZn. The corresponding processes on the polar Zn-terminated ZnO(0001) surfaces are found to have low or null barriers. Implications of these results for both MSR and low temperature mechanisms are discussed.

Sol-Gel Synthesis, Crystal Structure and Electronic Properties in Bi2+xAlxNi4-3xO7+δ (0.0 ≤ x ≤ 0.75) Composite Oxides

Sol-gel synthesis of Bi2+xAlxNi4-3xO7+δ (A1-A4: x = 0.0, 0.25, 0.50, 0.75) composite oxides were performed via nitrate-citrate route. Analysis of the powder XRD patterns by Fullprof shows cubic unit cell with lattice parameters in A1-A4: a = 10.2678, 10.1197, 10.1183, 10.1134 A; Z= 4 and space group Pm3n. Average crystallite sizes in A1-A4 determined by Scherrer’s relation are found to be in the range ~ 42-61 nm. The differential thermal analysis (DTA)/ thermogravimetric (TG) results show no phase transitions in the range 25-800 oC. The morphology of the samples characterized by scanning electron microscopy (SEM) show similar results with respect to the particle sizes and shapes. Rietveld refinement of the unit cell structure shows appreciably lowered agreement factors Rp, Rwp and Rexp for all the samples. The Bi-O and Ni-O bonds of different sites show marginal variations in the samples. Circular electron density contours around Ni and O due to valence orbitals shows the partial ionic character of Ni-O bonds. The plane-wave Density Functional Theory (DFT) calculations on crystal of structure of A1-A4 for band structure and density of states (DOS) using a CASTEP programme package show the valence band (VB) located at -8.0 to ~ 0.0 eV (Fermi level) predominantly comprised of O 2p orbitals overlapping with in-phase with Ni t2g , and the Bi 6s orbitals to form Ni-O-Bi bonds, and O 2p orbitals overlapping with Ni t2g or Bi 6s forming O-Ni-O or Bi-O-Bi bonds. The conduction band (CB) is composed of Ni eg orbitals, which narrows down with complete smearing of ~ 2.0 to 3.0 eV CB as in A1 in A2-A4 due to the absence of Al 3+ d orbitals. This result shows the transition of semiconductor-like as in A1 to metallic character with the Ni eg band predominantly crossing the Fermi level, in A2-A4. Research Article

Pathways for methanol steam reforming involving adsorbed formaldehyde and hydroxyl intermediates on Cu(111): density functional theory studies

Plane-wave density functional theory calculations have been carried out to explore possible pathways in methanol steam reforming (MSR) on Cu(111). We focus on reactions involving the adsorbed formaldehyde intermediate (CH(2)O) produced by methanol decomposition and the surface hydroxyl (OH) species generated by dissociative adsorption of H(2)O. Several possible pathways leading to the H(2) + CO(2) products have been identified. The two most likely pathways involve the formate (CHOO), rather than the carboxyl (COOH), intermediate, and they possess barriers lower than that of the rate-limiting step of MSR, namely the dehydrogenation of adsorbed methoxyl (CH(3)O) species.

CO2Adsorption on Carbon Models of Organic Constituents of Gas Shale and Coal

Imperfections of the organic matrix in coal and gas shales are modeled using defective and defect-free graphene surfaces to represent the structural heterogeneity and related chemical nature of these complex systems. Based upon previous experimental investigations that have validated the stability and existence of defect sites in graphene, plane-wave electronic density functional theory (DFT) calculations have been performed to investigate the mechanisms of CO(2) adsorption. The interactions of CO(2) with different surfaces have been compared, and the physisorption energy of CO(2) on the defective graphene adsorption site with one carbon atom missing (monovacancy) is approximately 4 times as strong as that on a perfect defect-free graphene surface, specifically, with a physisorption energy of ∼210 meV on the monovacancy site compared to ∼50 meV on a perfect graphene surface. The energy associated with the chemisorption of CO(2) on the monovacancy site is substantially stronger at ∼1.72 eV. Bader charge, density of states, and vibrational frequency estimations were also carried out and the results indicate that the CO(2) molecule binds to the surface becoming more stable upon physisorption onto the monovacancy site followed by the original C═O bonds weakening upon CO(2) chemisorption onto the vacancy site.

Periodic Density Functional Theory and Atomistic Thermodynamic Studies of Cobalt Spinel Nanocrystals in Wet Environment: Molecular Interpretation of Water Adsorption Equilibria

In this paper we present a theoretical study of water sorption on cobalt spinel nanocrystals by means of plane-wave periodic density functional theory (DFT) calculations jointly with statistical thermodynamics. The three most stable (100), (110), and (111) planes exposed by Co3O4 were considered, and their stabilization upon water adsorption is discussed in detail. The calculated changes in free enthalpy of the investigated system under different hydration conditions along with the Wulff construction were used to predict the rhombicuboctahedral equilibrium morphology of cobalt spinel nanocrystals in different conditions, which corresponds very well to the experimental transmission electron microscopic (TEM) images. Two-dimensional surface coverage versus temperature and pressure diagrams were constructed for each of the examined (100), (110), and (111) planes to illustrate water adsorption processes in a concise way.

Adsorption and activation of CO coadsorbed with K on Fe(100) surface: A plane-wave DFT study

The adsorption and diffusion properties of K atoms together with the coadsorption effects induced upon CO activation on Fe(100) surface have been studied using spin-polarized plane-wave density functional theory (DFT) calculations and the generalized gradient approximation. Preferential adsorption of K atoms takes place at surface hollow sites and diffusion among these sites has a small activation energy of only 0.7 kcal/mol. Substitutional adsorption of K at a surface Fe site is also possible but only at high temperatures required to overcome a barrier of about 36.0 kcal/mol. A systematic analysis of the modifications of binding properties for molecular (CO) and atomic (C,O) species upon interaction with K has been performed both as function of the relative separations as well as coverage using a series of (4 × 4), (3 × 3) and (2 × 2) supercell models. The presence of K leads to stabilization of both C and O species but in the last case significant variations were observed only when O is bonded at a bridge site. For CO molecule a relatively large range of stabilization energies can be induced by coadsorbed K depending on the relative CO–K separation and K coverage. The largest stabilization effects are observed at small separations, when K is located at a hollow site adjacent to CO binding site. In such cases the increase in binding takes place with important red shifts of CO vibrational frequency and with relatively large bond elongations, independent of CO binding mode on the surface. Relative to the bare surface, the presence of K was also found to reduce CO activation energies by as much as 6.2–7.8 kcal/mol, i.e. 25–31%, function of the relative separation and molecular coverage. Such effects have been correlated with the charge transfer from K to Fe surface and to CO molecule leading to an increased stabilization primarily of O and somewhat less of C species in the transition state and to reduction of the bond competition between CO and the surface atoms.

Density functional theory study of Fe, Co, and Ni adatoms and dimers adsorbed on graphene

Metal clusters have been investigated rather intensely for both fundamental and technological reasons. In this work we report the results of plane-wave density functional theory calculations of Fe, Co, and Ni adatoms and dimers adsorbed on graphene. We study both homonuclear and heteronuclear dimers, and the latter includes mixed dimers of Fe, Co, and Ni along with dimers of these elements with Pt. Our work is motivated by the fundamental interest in their configurational and magnetic properties. We calculated the adsorption site, the structure and relative stabilities of various adsorption configurations, the band structures, the atomic projected electronic density of states, and the magnetic moments of the adatoms and dimers. Contrary to previous work, our results show that adatoms bind weakly to graphene with binding energies ranging from 0.2 to 1.4 eV depending on the adsorption site and species. For both homonuclear and heteronuclear dimers the binding energies per atom are lower than the respective adatom cases, ranging from 0.1 to 0.5 eV per metal atom. The most strongly bound configurations for all the dimers studied are those with the dimer axis (nearly) perpendicular to the graphene plane and bound at the hole site. These configurations, which, to our knowledge, have not been considered in previous work, also turn out to have the largest enhancement of the magnetic moment at least for the atom farther from the graphene. The binding energies of these most strongly bound dimers are dependent on three factors, namely, the interconfigurational energy change in the dimer atom farther from graphene upon desorption, the charge transfer from the dimer to the graphene, and the adsorption site favored by the atom closer to the graphene sheet. The first factor is dominant for all the dimers studied here except for CoPt and NiPt. The relatively high electronegativity of Pt affects the character of the charge transfer from the dimer to graphene. In most of the dimers we investigated, charge is transferred almost exclusively from the dimer atom closer to the graphene except for heteronuclear dimers with Pt where charge is also transferred between the two dimer atoms upon adsorption. Thus, our calculations of the electronic structure allow us to understand the trends in binding energy and the magnetic moment in these dimers.

Atomic and Electronic Structure at Au/CdSe Interfaces

By means of plane-wave pseudopotential periodic-supercell density functional theory calculations with a gradient-corrected exchange-correlation functional, we investigated the formation and the electronic structure of thin Au overlayers on CdSe(0001) and CdSe(0001) surfaces. We explored several possible Au/CdSe interfaces, including nonstoichiometric cases in which the very interface layer is mixed, namely, contains atoms of both the metal and the semiconductor. The relative formation energies of the computed model structures indicate that the formation of a very thin Au layer on CdSe surfaces can be epitaxial in the very early deposition stages but only in rather Au-rich conditions. The analysis of the band structures, densities of states, and wave functions for the low-energy interfaces reveals that hybridization occurs between the metal and the semiconductor electron states. This hybridization is confined at the very interface and is not expected to have significant consequences on the plasmonic and excitonic excitations that are appealing for nanotechnology applications of metal-semiconductor nanoparticles.

Plane-Wave DFT Investigations of the Adsorption, Diffusion, and Activation of CO on Kinked Fe(710) and Fe(310) Surfaces

The adsorption, diffusion, and dissociation properties of CO on kinked Fe(710) and Fe(310) surfaces have been analyzed using spin-polarized plane-wave density functional theory (DFT) calculations within the generalized gradient approximation (GGA). Several one-, two-, three- and 4-fold binding configurations have been identified among which the preferential adsorption takes place at a 4-fold hollow site near the top of the step while the one with the smallest activation energy for dissociation is located at a 4-fold site near the bottom of the step. In the case of the individual atomic species, the adsorption takes place preferentially at the hollow site for the C atom and at the pseudo 3-fold site on the step for the O atom. By the increase in coverage, there is an overall decrease of the adsorption energies for either molecular (CO) or atomic (C,O) species. The diffusion barriers among different local minima at the steps or on the terraces of both surfaces have been determined, and their values were fou...

The dissociative adsorption of silane and disilane on Si(100)-(2×1)

We investigate the dissociative adsorption of silane and disilane on Si(100)-(2 x 1) using pseudopotential planewave density functional theory calculations. These are important steps in the growth of silicon films. Although silane has been studied computationally in some detail previously, we find physisorbed precursor states for the intradimer and interdimer channels. The silane energetics calculated here are in good agreement with experimental data and previous theoretical estimates and provide us with a useful reference point for our disilane calculations. Disilane has not been studied as intensively as silane. We investigate both silicon-silicon bond cleavage and silicon-hydrogen bond cleavage mechanisms, and for each we investigate intradimer, interdimer, and inter-row channels. As in the case of silane, we also find precursor states in the adsorption path in agreement with molecular beam experiments. The qualitative picture that emerges is that adsorption takes place through a weakly bound precursor state with a transition state to chemisorption that is low lying in energy relative to the gas phase. This is in good agreement with experimental data. However, the calculated energetics are only in fair agreement with experiments, with our transition state to chemisorption being about 0.02 eV above the gas phase while experimentally it is estimated to be approximately 0.28 eV below the gas phase. This suggests that accurate theoretical characterization of these weakly bound precursor states and the adsorption barriers requires further computational work.

An Unexpected Pathway for the Catalytic Oxidation of Methylidyne on Rh{111} as a Route to Syngas

This study investigates the adsorption properties of methylidyne (CH) on Rh{111}, its partial and full oxidation as well as its surface mobility, by means of plane-wave density functional theory (DFT) calculations. Besides investigating known oxidation pathways on rhodium, such as decomposition of CH and subsequent oxidation of the decomposition products, new pathways such as direct reaction of methylidyne and oxygen toward a surface aldyhyde-type species and the decomposition of this species are considered. The unexpected and novel pathway determined here by DFT is utilized for a microkinetic model of the formation of CO and CO2 from methylidyne. A comparison of this microkinetic study with experimental data shows that our novel mechanism can indeed describe the observations. This comparison strongly suggests that this new alternative route is the main reaction pathway for the conversion of methylidyne.

Derivation of Force Field Parameters for SnO2−H2O Surface Systems from Plane-Wave Density Functional Theory Calculations

Plane-wave density functional theory (DFT-PW) calculations were performed on bulk SnO2 (cassiterite) and the (100), (110), (001), and (101) surfaces with and without H2O present. A classical interatomic force field has been developed to describe bulk SnO2 and SnO2-H2O surface interactions. Periodic density functional theory calculations using the program VASP (Kresse et al., 1996) and molecular cluster calculations using Gaussian 03 (Frisch et al., 2003) were used to derive the parametrization of the force field. The program GULP (Gale, 1997) was used to optimize parameters to reproduce experimental and ab initio results. The experimental crystal structure and elastic constants of SnO2 are reproduced reasonably well with the force field. Furthermore, surface atom relaxations and structures of adsorbed H2O molecules agree well between the ab initio and force field predictions. H2O addition above that required to form a monolayer results in consistent structures between the DFT-PW and classical force field results as well.

Electron Emission from Diamondoids: A Diffusion Quantum Monte Carlo Study

We present density-functional theory (DFT) and quantum Monte Carlo (QMC) calculations designed to resolve experimental and theoretical controversies over the optical properties of H-terminated C nanoparticles (diamondoids). The QMC results follow the trends of well-converged plane-wave DFT calculations for the size dependence of the optical gap, but they predict gaps that are 1-2 eV higher. They confirm that quantum confinement effects disappear in diamondoids larger than 1 nm, which have gaps below that of bulk diamond. Our QMC calculations predict a small exciton binding energy and a negative electron affinity (NEA) for diamondoids up to 1 nm, resulting from the delocalized nature of the lowest unoccupied molecular orbital. The NEA suggests a range of possible applications of diamondoids as low-voltage electron emitters.