Ab Initio Density-functional Theory Calculations Research Articles

Chemical Reactions and Adsorption Geometries of Pyrrole on Ge(100)

The adsorption structures of pyrrole (C(4)H(5)N) on a Ge(100) surface at various coverages have been investigated with both scanning tunneling microscopy (STM) and ab initio density-functional theory (DFT) calculations. Three distinct features are observed in the STM images at low coverages. The comparison of the STM images with the simulation reveals that the most dominant flowerlike feature with a dark side is that the adsorbed pyrrole molecules with H dissociated form bridges between two down Ge atoms of neighboring Ge dimer rows through N-Ge bonding and beta-carbon-Ge interaction. The flowerlike feature without a dark side is also observed as a minority, which is identified as nearly the same structure as the most dominant one where a dissociated H is out of the feature. The third feature showing bright protrusions may be due to a C- and N-end-on (CN) configuration, where the pyrrole molecule is located on one dimer row. At higher coverages, the number of localized configurations increases.

Structure of Pyrrole on Ge(100)

The adsorption structures of pyrrole on a Ge(100) surface at low coverage have been investigated using ab initio density-functional theory (DFT) calculations. The most stable configuration is that the adsorbed pyrrole molecule with H dissociated forms a bridge between two down-Ge atoms of neighboring dimer rows through N–Ge bonding and C–Ge interaction. The corresponding simulated images explain well the flower-like features with a dark side observed in the experiment. Also, C–H dissociative structures are found to contribute as a minority to the features. A similar configuration to the most stable one, but with a dissociated H out of the region of interest, can explain the flower-like feature without a dark side. Finally, a C- and N-end-on configuration may be a possible candidate for bright protrusions in the STM images.

Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Relaxation of hot atoms following H2 dissociation on a Pd(111) surface

We study the relaxation of hot H atoms produced by dissociation of H2 molecules on the Pd111 surface. Ab initio density-functional theory calculations and the "corrugation reducing procedure" are used to determine the interaction potential for a H atom in front of a rigid surface as well as its modification under surface-atom vibrations. A slab of 80 Pd atoms is used to model the surface together with "generalized Langevin oscillators" to account for energy dissipation to the bulk. We show that the energy relaxation is fast, about 75% of the available energy being lost by the hot atoms after 0.5 ps. As a consequence, the hot atoms do not travel more than a few angstroms along the surface before being trapped into the potential well located over the hollow site.

1,2-Dibromoethyl-trichlorosilane (CH 2Br [sbnd]CHBr [sbnd]SiCl 3): conformational structure and vibrational properties by gas-phase electron diffraction, infrared and Raman spectroscopy, and ab initio molecular orbital and density functional theory calculations

The molecular structure and conformational properties of 1,2-dibromoethyl-trichlorosilane (CH 2Br CHBr SiCl 3) have been investigated using gas-phase electron diffraction (GED) data recorded at a temperature of 100 °C, together with ab initio molecular orbital (MO) and density functional theory (DFT) calculations, infrared (IR) and Raman spectroscopy in the liquid and solid phases, and normal coordinate analysis (NCA). The molecule exists in the gas- and liquid phases as a mixture of three conformers, gauche(−) [G(−)], with a refined torsion angle ϕ(BrCCBr) = −71(6)°, anti [A], with a torsion angle ϕ(BrCCBr) ≈ −170°, and gauche(+) [G(+)], with a torsion angle ϕ(BrCCBr) ≈ +70°. The second torsion angle of importance, the rotation about the C Si bond, has been refined to a value of +175(13)°. Torsion angles were only refined for the more abundant G(−) conformer. In the solid phase, only the G(−) conformer was observed. The temperature-dependent Raman spectra have provided an estimate of the relative conformational entropies, Δ S. The obtained composition from GED refinements was (%) G(−)/A/G(+) = 64(27)/23(13)/13(18) (values with estimated 2 σ uncertainties), giving a conformational stability order in agreement with both the Raman enthalpy measurements and the ab initio MO and DFT calculations using the 6-311G(d) basis set and scaled zero-point energies. Relevant structural parameter values obtained from the GED refinements (with the ab initio HF values used as constraints) were as follows (G(−) values with estimated 2 σ uncertainties): bond lengths ( r g): r(C C) = 1.501(18) Å, r(Si C) = 1.865(15) Å, r(〈C Br〉) = 1.965(8) Å (average), r(〈Si Cl〉) = 2.028(3) Å (average). Bond angles (∠ α): ∠CCSi = 114.1(33)°, ∠C 1C 2Br = 114.0(21)°, ∠〈CSiCl〉 = 109.6(7)° (average). Experimental IR/Raman and obtained vibrational wavenumbers based on both the unscaled, fixed-scaled as well as the scale-refined quantum-mechanical force fields [HF/6-311G(d)] are presented. The results are discussed and compared with some similar molecules from the literature.

Spatially Dependent Inelastic Tunneling in a Single Metallofullerene

We have measured the elastic and inelastic tunneling properties of isolated Gd@C(82) molecules on Ag(001) using cryogenic scanning tunneling spectroscopy. We find that the dominant inelastic channel is spatially well localized to a particular region of the molecule. Ab initio pseudopotential density-functional theory calculations indicate that this channel arises from a vibrational cage mode. We further show that the observed inelastic tunneling localization is explained by strong localization in the molecular electron-phonon coupling to this mode.

Comparative study of the monolayers A 3[sbnd]Si [sbnd](CH 2) n[sbnd]O [sbnd]CO [sbnd]CH 3 (A = Cl,OH) adsorpted on silica surface

Ab-initio density functional theory calculations have been carried out on the grafting of two different chains organosilane compounds on SiO 2 hydroxylated solid surfaces. The silica surface is modeled by a Si 12O 14H 24 trydimite based molecule. The organosilane chains to be grafted to the surface are the trihydroxysilanes and the trichlorosilanes with only few alkyls chains. The calculations have been performed with hybrid density functional (B3-LYP/6-31 + G**). Two final products are obtained and are stabilized with two types of interaction: a covalent bond Si O Si on one side of the chain and a hydrogen bond H O … O on the other side of the chain so that the chain lies flat to the surface. The electronic and geometrical properties of these grafted systems are studied. These results give new insight about the grafting of long chains organosilane on silica surfaces.

Stabilization of substitutional Mn in silicon-based semiconductors

We systematically investigate, using ab initio density-functional theory calculations, the properties of interstitial and substitutional Mn in both Si and Ge, as well as in the ${\mathrm{Si}}_{1\ensuremath{-}x}{\mathrm{Ge}}_{x}$ alloy. We show that volume effects are not the main reason Mn prefers to be a subsitutional impurity in pure Ge, and chemical effects, therefore, play an important role. Using realistic models of ${\mathrm{Si}}_{1\ensuremath{-}x}{\mathrm{Ge}}_{x}$, we show that for $x\ensuremath{\gtrsim}0.16$ substitutional Mn in Ge-rich neighborhoods become more stable than interstitial Mn, which may allow the growth of Si-based diluted magnetic semiconductors.

The Electric Field Gradient of 111Ag in Macrocyclic Crown Thioethers

Time differential perturbed angular correlation experiments and ab-initio density functional theory calculation were used to determine the electric field gradients of the metal centres of the macrocyclic crown thioethers Ag(15S5)[BF4], Ag(18S6-CH2OH)[CF3SO3], Ag(18S6)+, Ag(19S6-OH)[Tosylat] and Ag(20S6-OH)[CF3SO3]. The density functional theory calculations have been performed with the Amsterdam Density Functional code ADF. A “fingerprint system” is introduced, which allows to assign electric field gradients to certain Ag coordinations in these crown thioether complexes.

Electronic origin of structural trends across early transition-metal disilicides: Anomalous behavior ofCrSi2

We have investigated the structural stability of the early transition-metal disilicides $({\mathrm{TMSi}}_{2})$ using a hierarchy of electronic structure methods from the accurate ab initio to a simple $\mathrm{pd}$ tight-binding model. First, ab initio density-functional theory calculations provided excellent heats of formation and structural coordinates for the ${C11}_{b}$ ground state of ${\mathrm{MoSi}}_{2}.$ However, the $C40$ structure of ${\mathrm{CrSi}}_{2}$ was predicted to be less stable than ${C11}_{b}$ at absolute zero, indicating that the lattice entropy might stabilize the observed $C40$ phase. Second, less precise frozen-potential calculations allowed a Jones-type analysis of the structural stability in terms of the relative behavior of the densities of states. A $C5\stackrel{\ensuremath{\rightarrow}}{4}C4\stackrel{\ensuremath{\rightarrow}}{0}{C11}_{b}$ structure trend with increasing electron occupancy was found in good agreement with experiment. Finally, a very simple $\mathrm{pd}$ tight-binding model demonstrated that the structural trends were driven primarily by the $\mathrm{pd}\ensuremath{\pi}$ bond between the nearest-neighbor Si and TM atoms, reflecting the sensitivity of the $\ensuremath{\pi}$ bond order to dihedral angles.

Structure and energetics of polyhydroxylated carbon fullerenes

We have performed semiempirical modified-neglect-of-diatomic-overlap (to determine the most stable geometrical arrangements) as well as ab initio density-functional theory calculations (to obtain the electronic structure and total energies) at $T=0$ to analyze the energetics and structural properties of OH species adsorbed on the external surfaces of spheroidal ${\mathrm{C}}_{60}$ as well as on finite length open-ended armchair (6,6) and (8,8) carbon nanotubes. Interestingly we have found, for the low coverage regime, that the adsorbed OH groups prefer to organize as a hydroxyl cluster (having up to seven OH molecules) in only one side of the ${\mathrm{C}}_{60}$ surface. The observed clustering leads to the formation of a new amphiphilic molecule that naturally explains the stability of ${\mathrm{C}}_{60}(\mathrm{OH}{)}_{n}$ $(n\ensuremath{\sim}9\ensuremath{-}12)$ Langmuir monolayers at the air-water interface observed by several authors, where it is thus only the highly hydroxylated part of the carbon cage the one that dissolves in water slightly. For 8 to 14 adsorbed OH groups, a second hydroxyl island is gradually stabilized on the opposite side of the carbon structure, and finally, with increasing coverage the coexistence of ringlike and cluster arrays of OH groups seems to lead to the complete solubility of the carbon compound. In all cases, the OH molecules have been found to occupy on-top sites with a C-O-H bond tilted away from the surface normal and no hydrogen bond formation between the adparticles is obtained, in contrast to what is normally observed in the compact OH hexagonal phases stabilized on extended metal substrates. The calculated vibrational frequencies of our adsorbates have a good correspondence with the experimental measurements and provide a clear signature of the clustering of the OH molecules at low coverages. Finally, OH adsorption on the external surface of cylindrical carbon structures leads to the formation of quasi-one-dimensional molecular arrays, consistent with the synthesis of metal nanowires on the surface of carbon nanotubes, their length being determined by the length of the nanotube.

Evidence of a rutile-phase characteristic peak in low-energy loss spectra

Low-energy loss spectra (LELS) from electron energy loss spectroscopy (EELS) in a transmission electron microscope do not yield structural information as readily as do core loss spectra. In order to make LELS a more general technique, we have studied the 10--15 eV energy range in some $M{\mathrm{O}}_{2}$ compounds in great detail and identified a characteristic peak of a specific structural unit. A comparison of experimental EELS spectra and ab initio density-functional theory calculations (WIEN2K code) is presented. A definite peak around 14 eV appears in the imaginary part of the dielectric functions of those structures containing rutile units. These rutile units are ${M}_{3}{\mathrm{O}}_{15}$ clusters made of edge- and corner-sharing octahedra, which when stacked lead to rutile structures, among others. The peak is present in rutile phases with $M=\mathrm{Ti},$ V, Cr, Mn, Si, Ge, Sn, and Pb. Other structures, such as Ramsdellite or high-pressure ${\mathrm{TiO}}_{2}$ phases, also contain the necessary structural unit and indeed present the same feature. The origin of the peak can be elucidated by means of band structure calculations and an analysis of the orbitals involved in the transition. The existence of such a peak, always visible around 14 eV whatever $M,$ shows its remarkable universality.

Vanadium surface oxides on Pd(111): A structural analysis

Scanning tunneling microscopy studies of vanadium oxides grown on Pd(111) show interesting structures especially in the low-coverage region. Evaporation of V in an oxygen background at elevated sample temperature $(250\ifmmode^\circ\else\textdegree\fi{}\mathrm{C})$ results in the formation of a nonperiodic honeycomb-like structure growing from the steps, which starts to transform into an ordered phase at a vanadium coverage of $\ensuremath{\approx}0.2\mathrm{ML}$ (monolayer). At 0.31 ML the entire surface is covered by this well-ordered open $(4\ifmmode\times\else\texttimes\fi{}4)$ structure. Annealing this structure in ${\mathrm{H}}_{2}$ atmosphere transforms the phase into a ${\mathrm{V}}_{2}{\mathrm{O}}_{3}$ surface oxide with $(2\ifmmode\times\else\texttimes\fi{}2)$ periodicity, whose optimal coverage is reached at 0.5 ML vanadium. Models for both ordered structures have been suggested before on the basis of ab initio density-functional theory (DFT) calculations and molecular-dynamics simulations and these models are now unambiguously confirmed by quantitative low-energy electron-diffraction (LEED) analyses. In the $(4\ifmmode\times\else\texttimes\fi{}4)$ phase, the V atoms are surrounded by four oxygen atoms in an unusual tetrahedral coordination leading to a ${\mathrm{V}}_{5}{\mathrm{O}}_{14}$ stoichiometry. This tetrahedral coordination allows the oxide to adopt open loosely packed two-dimensional (2D) and 1D structures, which are stabilized by the surface-oxide interface energy. Furthermore, it is shown that state of the art DFT calculations can indeed predict complex structures exactly as well as that modern quantitative LEED is capable of dealing with very large unit cells.

Free-energy calculations of intrinsic point defects in silicon

We study the energetics of various point defects in silicon using ab initio density-functional methods. The formation free energies are calculated from the harmonic phonon frequencies, which are determined from ab initio density-functional perturbation theory calculations. We deduce the concentrations of defects as a function of temperature and compare them with experimental estimates. The localized vibrational modes associated with the various defects are described.

Contrasting bonding behavior of thiol molecules on carbon fullerene structures

We have performed semiempirical as well as ab initio density-functional theory (DFT) calculations at $T=0$ to analyze the equilibrium configurations and electronic properties of spheroidal ${\mathrm{C}}_{60}$ as well as of cylindrical armchair (5,5) and (8,8) fullerenes passivated with ${\mathrm{SCH}}_{3}$ and $\mathrm{S}({\mathrm{CH}}_{2}{)}_{2}{\mathrm{CH}}_{3}$ thiols. Our structural results reveal that the lowest-energy configurations of the adsorbates strongly depend on their chain length and on the structure of the underlying substrate. In the low-coverage regime, both ${\mathrm{SCH}}_{3}$ and $\mathrm{S}({\mathrm{CH}}_{2}{)}_{2}{\mathrm{CH}}_{3}$ molecules prefer to organize into a molecular cluster on one side of the ${\mathrm{C}}_{60}$ surface, providing thus a less protective organic coating for the carbon structure. However, with increasing the number of adsorbed thiols, a transition to a more uniform distribution is obtained, which actually takes place for six and eight adsorbed molecules when using $\mathrm{S}({\mathrm{CH}}_{2}{)}_{2}{\mathrm{CH}}_{3}$ and ${\mathrm{SCH}}_{3}$ chains, respectively. In contrast, for the tubelike arrangements at the low-coverage regime, a quasi-one-dimensional zigzag organization of the adsorbates along the tubes is always preferred. The sulfur-fullerene bond is considerably strong and is at the origin of outward and lateral displacements of the carbon atoms, leading to the stabilization of three-membered rings on the surface (spheroidal structures) as well as to sizable nonuniform radial deformations (cylindrical configurations). The electronic spectrum of our thiol-passivated fullerenes shows strong variations in the energy difference between the highest occupied and lowest unoccupied molecular orbitals as a function of the number and distribution of adsorbed thiols, opening thus the possibility to manipulate the transport properties of these compounds by means of selective adsorption mechanisms.

Intrinsic nanoscale phase separation of bulk As2S3 glass

Raman scattering on bulk As x S1− x glasses shows that vibrational modes of As4S4 monomer first appear near x = 0.38, and their concentration increases precipitously with increasing x, suggesting that the stoichiometric glass (x = 0.40) is intrinsically phase separated into small As-rich (As4S4) and large S-rich clusters. Support for the Raman-active vibrational modes of the orpiment-like and realgar-like nanophases is provided by ab-initio density functional theory calculations on appropriate clusters. Nanoscale phase separation provides a basis for understanding the global maximum in the glass transition temperature T g near x = 0.40, and the departure from Arrhenius temperature activation of As2S3 melt viscosities.

N,N-Dimethylthioformamide and N,N-Dimethylthiocarbamoyl Chloride: Molecular Structure by Gas-Phase Electron Diffraction and ab Initio Molecular Orbital and Density Functional Theory Calculations

The molecular structures and the dimethyl rotamer properties of N,N-dimethylthioformamide (TFA) and N,N-dimethylthiocarbamoyl chloride (TCC) have been investigated using gas-phase electron diffraction (GED) data recorded at a temperature of 25 °C, together with ab initio molecular orbital (MO) and density functional theory (DFT) calculations, as well as normal coordinate analysis (NCA) using MP2/6-31+G(d,p) scaled force fields. The molecules exist in the gas phase as a single near-planar conformer, not exhibiting true Cs symmetry. The orientation of the two methyl groups on the nitrogen atom have been closely examined by ab initio MO and DFT calculations, and these have been found to be oriented differently in the two molecules. Relevant structural parameter values obtained from the GED refinements, using values from the MP2/6-31+G(d,p) calculations as constraints, were as follows (values under C1 symmetry assumption with estimated 2σ uncertainties): For TFA, bond lengths (rg) were r(CS) = 1.649(2) Å, r(C2−N) = 1.346(3) Å, r(〈C5,9−N〉) = 1.463(2) Å (av), r(〈C−H〉) = 1.125(4) Å (av), bond angles (∠α) were ∠NC2S = 127.0(3)°, ∠〈C2NC5,9〉 = 121.8(5)° (av), ∠〈NC5,9H〉 = 110.4(7)°, and torsion angle φ1(S3−C2−N1−C5) = 12.8° ± 2.7°. For TCC, bond lengths (rg) were r(CS) = 1.641(3) Å, r(C2−N) = 1.348(4) Å, r(C2−Cl) = 1.772(4) Å, r(〈C5,9−N〉) = 1.472(3) Å (av), r(〈C−H〉) = 1.109(8) Å (av), bond angles (∠α) were ∠NC2S = 127.4(6)°, ∠〈C2NC5,9〉 = 122.0(6)° (av), ∠〈NC2Cl〉 = 113.0(4)°, and torsion angle φ1(S3−C2−N1−C5) = −5.5° ± 10.1°. The results are discussed and compared with the oxygen analogues and previous results for the TCC molecule, as well as with similar molecules in the literature.

Ab initio studies of quasi-one-dimensional pentagon and hexagon ice nanotubes

Ab initio plane-wave total-energy calcuation is carried out to study the relative stability of the quasi-one-dimensional (Q1D) pentagon and hexagon ice nanotubes. Electronic structure calculations indicate the two Q1D ice nanotubes have nearly the same band structures and energy bandgap as those of proton-ordered bulk ice Ih. Ab initio molecular-orbital and density-functional theory calculations, as well as three classical potential models of water, are also employed to investigate the relative stability of the pentagon and hexagon water clusters (H2O)30, (H2O)60, and (H2O)120. Clusters of this kind can serve to bridge the gap between the small polygonal water rings and the infinitely long Q1D polygon ice nanotubes. It is found that the polygon water prisms with the size (H2O)120 begin to show the relative energetic behavior of the infinitely long polygon ice nanotubes.

Clustering ofH2molecules encapsulated in fullerene structures

We have performed semiempirical (MNDO) as well as ab initio density-functional theory calculations at $T=0$ to analyze the hydrogen storage behavior in spheroidal ${\mathrm{C}}_{60}$ and ${\mathrm{C}}_{82},$ and cylindrical finite-length (5,5) armchair C and BN fullerenes. We have found that, while chemisorption of individual H atoms to the external surface of the fullerenes is observed, hydrogen atoms cannot be attached to the inner wall of the structures and can only exist in a molecular form inside the fullerenes. We further find that, as a function of the symmetry of the encapsulating cavity and a delicate balance between repulsive energies among ${\mathrm{H}}_{2}$ molecules inside the structures and those between ${\mathrm{H}}_{2}$ molecules and the fullerene walls, molecular $({\mathrm{H}}_{2}{)}_{N}$ clusters of well defined shape are formed namely: linear configurations, two-dimensional zig-zag and triangular arrays, and three-dimensional structures such as octahedral and icosahedral clusters, as well as helicoidal cylindrical-shape assemblies. In the cylindrical configurations (C and BN tubes), hydrogen atoms are placed inside the structures up to a bond breakage of the fullerene network, which allow us to estimate the maximum storage capacities of the different configurations. Actually, in our closed nanotubes, we relate the bond breakage mechanism to the development of a nonuniform hydrogen accommodation along the tubes, driven by the both highly anisotropic ${\mathrm{H}}_{2}\ensuremath{-}{\mathrm{H}}_{2}$ and wall-${\mathrm{H}}_{2}$ repulsive interactions. With increasing the number of stored ${\mathrm{H}}_{2},$ tubes are found to be mainly radially deformed, a fact that reduces (up to $\ensuremath{\sim}13%)$ the energy difference between the highest occupied and lowest unoccupied molecular orbitals in the structures. Finally, saturation of the tube ends with molecular terminations results in stable compounds from which a density-controlled storage of hydrogen seems to be possible.

Ab initiobased modeling of III-V semiconductor surfaces: Thermodynamic equilibrium and growth kinetics on atomic scales

We present a general methodology for developing predictive atomistic models of III-V semiconductor surfaces. We apply this methodology to the development of a kinetic Monte Carlo model that describes both equilibrium and growth of InAs(001) surfaces. Thermodynamic equilibrium behavior is solely based on ab initio density-functional theory calculations. Inclusion of kinetic processes and a large set of atomistic configurations on this highly complex surface enables the correct prediction of several experimental trends, including two thermodynamically stable surface reconstructions in the As-rich regime.