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Transition-metal containing metal phthalocyanine (MPc) molecules are representative molecular magnets and their adsorption on two-dimensional metallic surfaces has been extensively studied. In/Si(111)-4×1 is a prototypical quasi-one-dimensional metallic surface made up of alternating In nanowires and Si Seiwatz chains. Here, we investigated the adsorption of MPc (M = Mn, Fe, Co) on In/Si(111)-4×1 using density functional theory calculations. We found that there are three locally stable adsorption sites of MPc, two on In nanowires and one on Seiwatz chains. Also, the stable orientation of MPc is different depending on adsorption sites. Among three MPc’s, MnPc are found to carry a finite magnetic moment of 1.6 ~ 2.1 μB in its three almost-degenerate adsorption structures. The interaction between MPc molecules and the In/Si(111)-4×1 surface turns out to occur via the charge transfer, and the charge transfer channel varies for different adsorption sites: Transition-metal 3dz2 and two N 2pz orbitals on In nanowires vs. four N 2pz orbitals on Seiwatz chains.

One-dimensional indium chains on Si(111) exhibit both temperature-and defect-induced perioddoubling (×2) structural transitions, and their natures have been focus of recent investigations. Using density functional perturbation theory calculations, we examined the vibrational properties of the room-temperature Si(111)In-4×1 structure. The phonon band structure revealed two unstable modes at the zone-boundary in the chain direction, which lead to a lattice instability towards a structure with parallel trimers. This lattice-instability-driven 4 × 2 structure is different from the low-temperature 4×2 (LT-4×2) structure (hexagon structure). The result suggests that the roomtemperature phase is neither a static 4×1 phase nor the dynamical fluctuation of the LT-4×2 phase. We demonstrate that the room-temperature phase is a dynamically fluctuating parallel-trimer 4×2 phase, and the fluctuations become suppressed near the defects to result in the defect-induced ×2 structure.

Recent studies on a quasi-one-dimensional (quasi-1D) charge-density-wave (CDW) system, In atomic wires on Si(111), have brought intriguing issues on topological solitons in quasi-1D systems: the existence of few-atom-sized solitons, chirality of solitons, and the realization of logic exploiting the chirality switching. Using scanning tunneling microscopy and first-principles calculations, we show that the previously reported ``short'' phase-flip defects are In adatoms and thus have nonsolitonic nature, resolving the controversy over the existence of highly localized solitons. The observed ``long'' phase-flip and phase-slip defects are genuine solitons with and without chirality, respectively. While achiral solitons (phase-slip defects) can exist on the pristine CDW ($8\ifmmode\times\else\texttimes\fi{}2$) surface, chiral solitons (phase-flip defects) cannot due to their breakage of $8\ifmmode\times\else\texttimes\fi{}2$ ordering. The chiral solitons can exist only when they are trapped by In adatoms and constitute a part of a closed-loop domain wall. The intertwinement of chiral solitons and In adatoms implies the limitations of the previously proposed logic utilizing soliton chirality, but it provides an opportunity to realize this by controlling the In-adatom defect.

We report density functional theory calculations on the vacancy-induced magnetic properties of the wurzite GaN $$(10\bar 10)$$ surface. Among various intrinsic vacancies on the surface, we focus on the monatomic Ga and N vacancies. We have found two stable geometries of a surface Ga vacancy and one stable geometry of a surface N vacancy. Two stable surface Ga vacancy structures are shown to have magnetic moments of 3 μ B , which is the same as for the bulk Ga vacancy. Differently from the bulk N vacancy carrying null magnetic moment, the monatomic surface N vacancy has a finite magnetic moment of 1 μ B . These results support the experimental claim that the roomtemperature ferromagnetism observed in inorganic nanoparticles is due to surface vacancies and their complexes. We also present simulated scanning tunneling microscope images for comparison with those obtained in future experimental studies.

We report density-functional-theory calculations on vacancies on the ZnO\((10\bar 10)\) surface with the on-site Coulomb interaction correction. Zn and O vacancies and three different configurations of ZnO divacancies were examined considering all the possible charge states. Using the calculated vacancy formation energies, we constructed the phase diagram by spanning the allowed range of electronic and ionic chemical potential. Differently from the bulk where the divacancy is not stabilized at all, one configuration of surface divacancies can be stable in a certain region of the chemical potentials. Among all the stable vacancies, only the neutral and the singly negatively-charged monatomic Zn vacancies exhibit a finite magnetic moment of 1 μB, which implies that the surface Zn vacancies may be responsible for the experimentally-observed room-temperature ferromagnetism in ZnO nanocrystals.

We have investigated the vibrational properties of orthorhombic PtSi by performing first-principles calculations. The calculated phonon band structure shows unstable phonon modes around the Γ-point. The ionic displacement vectors associated with the unstable Γ-point phonon mode suggest a structural modulation to a lower-symmetry phase, which was confirmed by comparing the theoretical equations of states of the modulated (P212121) and the unmodulated (Pnma) PtSi. The symmetry-reduced modulated orthorhombic PtSi shows a phonon band gap. We attribute the origin of the phonon band gap to the separation of the low-frequency Pt phonon modes and the high-frequency Si phonon modes due to the large atomic mass difference between Pt and Si.

We report density functional theory calculations for the bulk ZnO divacancy in hexagonal ZnO and compare the results with the monatomic bulk vacancies. We find that the ZnO divacancy could be viewed as a tightly-bound state of a doubly-negative Zn vacancy and the doubly-positive O vacancy from the structural and the electronic points of view. The singly-positive ZnO divacancy is found to carry a magnetic moment of 1µB, but it can only be stabilized in very high p-type samples. Otherwise, the non-magnetic neutral divacancy is stable. These results suggest that the ZnO divacancies in the bulk region cannot play a significant role in stabilizing the recently-observed ferromagnetism in ZnO nanoparticles.

We investigated the structural and the binding properties of black phosphorus (black-P) by employing density functional theory (DFT) calculations in combination with various implementations of the van der Waals (vdW) interaction. Both the binding energy curve of the two isolated puckered layers and the equation of states of the bulk black-P suggest that the conventional generalized gradient approximation (GGA) functional is incapable of describing the interlayer vdW interaction. From the comparison of the seven different vdW implementations, the appropriate vdW schemes in describing layer-structured black-P are found to be either the Grimme’s dispersion correction (DFT-D2) or the optB86b vdW denisty-functional approach.

We have performed spin-polarized density functional theory calculations on κ-carbides, (Fe, Mn)3AlC, to investigate both the effect of different exchange-correlation functionals and the effect of Mn substitution. Differently from our previous calculations using the Perdew-Wang functional, Fe2MnAlC is found to be the most stable crystal among crystalline κ-carbides by using the Perdew, Burke, and Ernzerhof functional. Supercell calculations to simulate low Mn concentration show that substitutional Mn atoms hardly interact with each other and suggest that a random alloy model can be applied. The stabilization of Fe2MnAlC and its enhanced magnetization are attributed to the formation of a -Mn-C- linear chain structure.

We perform spin-polarized density functional theory calculations for a Zn vacancy on the ZnO(10 $\bar 1$ 0) surface. Two stable configurations of the surface Zn vacancy are found, and the activation energy barrier is estimated to be ∼0.01 eV. The lower energy configuration has a newly formed surface Zn-O bond to restore the bulk-like structure on the surface. Due to the newly formed bond, the vacancy state in the band gap is characterized by a complicated hybridization of neighboring surface and subsurface atoms and by a more extended electron density. Despite such a hybridization, the surface Zn vacancy is found to have a robust magnetic moment of 1 μ B , implying that surface Zn vacancies may be responsible for the ferromagnetism observed in ZnO thin films and nanoparticles. Simulated scanning tunneling microscope images show that the two structures of the surface Zn vacancy can be distinguished in the filled-state images.

The initial adsorption of oxygen molecules on Si(001) is investigated at room temperature. The scanning tunneling microscopy images reveal a unique bright O2-induced feature. The very initial sticking coefficient of O2 below 0.04 Langmuir is measured to be ∼0.16. Upon thermal annealing at 250–600 °C, the bright O2-induced feature is destroyed, and the Si(001) surface is covered with dark depressions that seem to be oxidized structures with -Si-O-Si- bonds. This suggests that the observed bright O2-induced feature is an intermediate precursor state that may be either a silanone species or a molecular adsorption structure.

The Cl-saturated Si(001) surface is investigated by employing density functional theory calculations. From the electronic density of states, the low- and the high-bias filled-state images and the empty-state images are found to originate from Cl(3p) states directed in-plane, in parallel with the Si dimer row, and perpendicular to the surface (z), respectively. The bright triplet, which is a characteristic scanning tunneling microscopy (STM) feature of an unchlorinated bare Si dimer, is attributed to an occupied dangling bond state of the bare Si dimer that is hybridized with the neighboring Cl(3pz) orbital. The previously observed split-dimer feature is confirmed to be the dimer-bond oxidized structure. Finally, we suggest that the initial back-bond oxidation does not occur on the chlorinated Si(001) surface because it is energetically not favored compared with dimer-bond oxidation and because its STM simulation does not match experimental images.

We investigated the structural and the binding properties of tetrahedral P4 molecular pairs by employing density functional theory (DFT) calculations using both the local density approximation (LDA) and the generalized gradient approximation (GGA). To consider the van der Waals interaction, we employed the GGA with dispersion correction, specifically Grimme’s approach (DFT-D2). This DFT-D2 in conjunction with the GGA (GGA-D2) well fixes the failure of the GGA in reproducing a reasonable binding energy curve. The binding energy and the equilibrium intermolecular distance are found to be in close correlation with the number of adjacent atomic pairs between two molecules. Application of the LDA and the GGA-D2 to a molecular crystal β-P4 and comparison with experiments confirms that the GGA-D2 should be used for a reliable description of P4-based molecular systems.

We present our ab initio results on carbon nanotubes functionalized with dichlorocarbene (CCl2). We find that the electronic properties of carbon nanotubes are significantly modified depending on the site of [2 + 1] cycloaddition. The random addition of dichlorocarbene is found to reduce the band gap of semiconducting nanotubes while those of metallic nanotubes are increased. This is related to the quasi-bound states within the energy gap originated from dichlorocarbene, which are revealed at the large supercell calculation. 2005 Elsevier B.V. All rights reserved.

We have performed total-energy density-functional calculations using ab initio pseudopotentials to investigate the atomic geometry and scanning tunneling microscopy (STM) of K adsorbed on the InAs(110) surface. We have identified the most favorable adsorption geometry formed by K adatoms occupying two almost degenerate adsorption sites. Based on this structure, we have simulated the STM images showing asymmetric and zigzag chain along the [ 1 1 ¯ 0 ] direction for both negative and positive sample biases. The calculated STM images agree with the recent STM observation.

SIMS quantification and depth scale calibration has been based on ion implanted standards. In this work, the feasibility of using multiple delta layer reference materials for quantitative SIMS depth profiling is tested and presented. Preliminary studies on application of multiple As delta layer Si thin films to shallow junction analysis will be presented and discussed.

We report pseudopotential density-functional calculations of the “3 ×1” phase of the Ba/Si(111) surface. To resolve the coverage issue of the Ba/Si(111) surface, we investigate various structural models with two Ba coverages: 1/3 ML and 1/6 ML. Based on the comparison of the simulated STM images for two coverages and the experimental images, it is found that the “3 ×1” phase has 1/6 ML Ba and a 3 ×2 structure with the honeycomb chain-channel Si reconstruction. The substrate reconstruction is quite similar to the Si(111)-3 ×1 surface induced by 1/3 ML alkali-metals. The experimental semiconducting band gap is well reproduced by the LDA band structure.

We discuss our new implementation of the Real-space Electronic Structure method for studying the atomic and electronic structure of infinite periodic as well as finite systems, based on density functional theory. This improved version which we call HARES (for High-performance-fortran Adaptive grid Real-space Electronic Structure) aims at making the method widely applicable and efficient, using high performance Fortran on parallel architectures. The scaling of various parts of a HARES calculation is analyzed and compared to that of plane-wave based methods. The new developments that lead to enhanced performance, and their parallel implementation, are presented in detail. We illustrate the application of HARES to the study of elemental crystalline solids, molecules and complex crystalline materials, such as blue bronze and zeolites., Comment: 17 two-column pages, including 9 figures, 5 tables. To appear in Computer Physics Communications. Several minor revisions based on feedback

We have determined the structure of AlSb and GaSb (001) surfaces prepared by molecular beam epitaxy under typical Sb-rich device growth conditions. Within the range of flux and temperature where the diffraction pattern is nominally $(1\ifmmode\times\else\texttimes\fi{}3)$, we find that there are actually three distinct, stable $(4\ifmmode\times\else\texttimes\fi{}3)$ surface reconstructions. The three structures differ from any previously proposed for these growth conditions, with two of the reconstructions incorporating mixed III-V dimers within the Sb surface layer. These heterodimers appear to play an important role in island nucleation and growth.

A Comment on the Letter by Wall et al. [Phys. Rev. Lett. 109, 186101 (2012)]. The authors of the Letter offer a Reply.

The existing 'residual minimization/direct inversion in the iterative subspace' (DIIS) method for the iterative calculation of low-lying eigenstates of a large matrix is further developed and modified. The DIIS method, which uses the residual minimization criterion, may fail to provide correct low-lying eigenspectra in the case of ill-formed matrices, e.g. the momentum-space representation of Hamiltonian matrices of systems containing transition metal, rare earth, or first-row elements. We suggest the inclusion of another criterion-the vanishing of the overlap integral of an iterative eigenvector with already obtained low-lying eigenvectors in order to prevent the eigenvector from collapsing to lower states. Two numerical examples of the success of our modified DIIS method in contrast to the failure of the conventional DIIS method are presented.

We have recorded the x-ray diffraction (XRD) patterns of nanometer-size W metal clusters prepared at different average cluster sizes. Nanometer-size W metal clusters were produced through a collision induced clustering mechanism of W metal atoms generated by decomposing W(CO)6 vapors. The XRD patterns clearly showed that structure changed from amorphous→face- centered-cubic (fcc)→body-centered-cubic (bcc) with increasing average cluster size. This implies that W metal clusters do not simply approach the bulk bcc structure but pass through an intermediate fcc structure before they reach the bulk structure, as predicted by Tomanek, Mukherjee, and Bennemann [Phys. Rev. B 28, 665 (1983)].

An exchange of hydrogen-bond and coordinate covalent-bond (dative-bond) interactions is found to play a critical role in the self-assembly of ${\mathrm{NH}}_{3}$ molecules on the Si(001) surface. An ${\mathrm{NH}}_{3}$ molecule in the height of $\ensuremath{\sim}3--10\text{ }\text{ }\AA{}$ above the surface is attracted toward the preadsorbed ${\mathrm{NH}}_{2}$ moiety through the long-range H-bond interaction. Within $\ensuremath{\sim}3\text{ }\text{ }\AA{}$, the H-bond interaction becomes repulsive, and instead the dative bond with the buckled-down Si atom governs the adsorption process. The interplay of the two interactions induces the clustering and the zigzag feature of the dissociatively adsorbed ${\mathrm{NH}}_{3}$ molecules on the Si(001) surface.

Point defects on a $\mathrm{Si}(001)\ensuremath{-}(2\ifmmode\times\else\texttimes\fi{}1)$ surface were examined by scanning tunneling microscopy and ab initio pseudopotential calculations. The residual water molecules in the ultrahigh vacuum chamber are found to be the sole origin of the type-$C$ defects. Most of the apparent dimer vacancies in the filled-state images were found to show a distinct $U$-shaped triple-dimer footprint in the empty-state images, which also originate from water adsorption. These two defects were identified as a single dissociated water molecule forming Si-OH and Si-H bonds in the interdimer (type-$C$ defect) and the on-dimer (dimer-vacancy-like or $U$-shape defect) configurations.

Impurities interact with a charge density wave (CDW) and affect the phase transitions in low-dimensional systems. By using scanning tunneling microscopy, we visualize the interaction between oxygen impurities and the CDW in indium atomic wires on Si(111), a prototypical one-dimensional electronic system, and unveil the microscopic mechanism of the intriguing O-induced increase of the transition temperature (Tc). Driven by the fluctuating CDW, the O atoms adopt an asymmetric structure. By adjusting the asymmetry, a pair of O impurities in close distance can pin the one-dimensional CDW, which develops into the two-dimensional domains. First-principles calculations showed that the asymmetric interstitially-incorporated O defects induce shear strains, which assists the formation of hexagon structure of the CDW phase. The cooperative interplay between the O impurities and the CDW is responsible for the enhancement of the CDW condensation and the consequent increase in Tc.

Using a Green function method based on an atomic vibration model, herein we report the results from our investigation of phonon transport through multiple Si/PtSi layered structures. In contrast with values predicted using elastic wave theory and an impedance mismatch method, we find that a detailed atomic-vibration approach exhibits significantly suppressed phonon transport and leads to a 30-times reduction of the thermal conductance, compared to that of Si bulk. We attribute the origin of the suppression to the lack of PtSi phonon modes in the energy range of 20–30 meV, and to the effects of interface scattering between Si and PtSi layers.

The C amount and the structure of the $\mathrm{S}\mathrm{i}(001)\mathrm{\text{\ensuremath{-}}}c(4\ifmmode\times\else\texttimes\fi{}4)$ surface is studied using scanning tunneling microscopy (STM) and ab initio calculations. The $c(4\ifmmode\times\else\texttimes\fi{}4)$ phase is found to contain $1/8$ monolayer C (1 C atom in each primitive unit cell). From the C amount and the symmetry of high-resolution STM images, it is inferred that the C atoms substitute the fourth-layer site below the dimer row. We construct a structure model relying on ab initio energetics and STM simulations. Each C atom induces an on-site dimer vacancy and two adjacent rotated dimers on the same dimer row. The $c(4\ifmmode\times\else\texttimes\fi{}4)$ phase constitutes the subsurface ${\mathrm{S}\mathrm{i}}_{0.875}{\mathrm{C}}_{0.125}$ $\ensuremath{\delta}$ layer with two-dimensionally ordered C atoms.

We present a dynamic pathway model for the formation of C(60) using the action-derived molecular dynamics simulations. We propose candidate precursors for dynamic pathway models in which carbons spontaneously aggregate due to favorable energetics and kinetics. Various planar polycyclic models are in a disadvantageous state where they cannot be trapped in the forward reaction due to their high excess internal energies. Our simulation results show that precursors either in the shape of tangled polycyclics or in the shape of open cages are kinetically favored over precursors in the shape of planar hexagonal graphite fragments. Calculated activation energies for the probable precursor models are in good agreement with experiment. Existence of chains in the models of tangled polycyclics and open cages is beneficially for the formation of C(60) molecule. Chains attached to the precursor model are energetically favorable and display lithe movements along the dynamic pathway.

We investigate the initial stage of the C incorporation into Si(001) using thermal dissociation of ${\mathrm{C}}_{\mathrm{2}}{\mathrm{H}}_{\mathrm{2}}$. The scanning tunneling microscopy shows that C-induced dimer vacancies (DVs) with depressed adjacent dimers are generated on the surface and aligned in the dimer direction, forming the $2\ifmmode\times\else\texttimes\fi{}n$ structure. The ab initio pseudopotential calculations reveal that, with the presence of a DV in the surface, the $\ensuremath{\alpha}$ site in the fourth subsurface layer directly below the DV is the most favorable for the incorporated C atoms. The embedded C atoms align one dimensionally due to the interaction which is attractive in neighboring dimer rows but repulsive in the same dimer row.

The $\mathrm{Ba}/\mathrm{Si}(111)$ surface, previously known as a $3\ifmmode\times\else\texttimes\fi{}1$ phase, is found to have a $3\ifmmode\times\else\texttimes\fi{}2$ periodicity and a semiconducting band gap. The substrate reconstructs into the honeycomb chain-channel (HCC) structure with Ba atoms in the channel, as in the alkali-metal-induced $\mathrm{Si}(111)\ensuremath{-}(3\ifmmode\times\else\texttimes\fi{}1)$. However, the metal coverage is determined to be 1/6 monolayers, half the alkali-metal coverage. We propose that the structure and the metal coverage determined for the Ba adsorbate is universal for other alkaline-earth-metal adsorbates. With the alkali-metal-induced $3\ifmmode\times\else\texttimes\fi{}1$ case, our results lead to a rule that one donated electron per $3\ifmmode\times\else\texttimes\fi{}1$ surface unit is necessary to stabilize the HCC reconstruction of Si.

Based on density-functional theory calculations, the effects of cation compositions on electronic structures of In-Sn-Zn-O amorphous semiconductors were investigated. We considered various composition ratios of In, Sn, and Zn in O stoichiometric condition, and found that the conduction band minimum (CBM) energy level decreases and the valence band tail (VBT) energy level extent increases as the sum of In and Sn ratios (RIn+RSn) increases. The CBM lowering is attributed to the increased overlap of the In-5s and Sn-5s orbitals as the RIn+RSn increases, and correspondingly the electron effective masses (me*) are found to be reduced. The VBT increase is found to be due to the increased density of the In and Sn atoms, near which the O-2p inter-site ppσ* coupling is larger than that near the Zn atoms. The acute O-(In,Sn)-O angles are suggested to be structurally important, giving the stronger O-O ppσ* coupling.

We investigate the maximum available free electron carrier density in Al-doped n-type ZnO, based on density-functional theory calculations. The Coulomb interactions between the Al dopants and the Zn-vacancy native acceptors are found to limit the carrier density. In typical growth conditions, the n-type doping limit is found to be in the range of 1019 ∼ 1021 cm−3.

The atomic and electronic structure of an As vacancy on the GaAs(110) surface is examined using ab initio pseudopotentials. The relaxed atomic structure reveals an inward movement of the neighboring surface Ga atoms which is in disagreement with recent interpretations of the scanning tunneling microscopy (STM) images for this system. However, a careful analysis of the wave-function character of the vacancy states, and the theoretical STM image, for this geometry yields excellent agreement with the experimental STM images.

We studied the vacancy-induced ferromagnetism in bulk and at the (1010) surface of wurtzite ZnO using density functional theory calculations. It is found out that surface vacancies are energetically favored to bulk vacancies and that the ferromagnetism is induced by Zn vacancies but not by O vacancies. Moreover, local magnetic moments induced at O atoms adjacent to the Zn vacancy are calculated to be larger on the surface than in bulk. These findings indicate that Zn vacancies at surfaces are responsible for the experimentally observed room-temperature ferromagnetism in undoped ZnO thin films and nanoparticles.

The structural properties and magnetic phase stability of Fe(x)Pt(1−x) alloys in L12 crystal structure in bulk as well as thin film on Pt (110) substrate are studied by means of the highly precise full-potential linearized augmented plane-wave method within generalized gradient approximation. The antiferromagnetic (AFM) phase is found to be preferred over the ferromagnetic (FM) phase for FePt3 bulk alloy in agreement with experiment while FexPt(1−x), where x=0.25 and 0.5 with a film thickness smaller than 0.5nm, favor the FM phase. The total energy calculation assuming pseudomorphic strain reveals that the AFM preference for bulk is maintained in wide range of tetragonal distortion up to the value of 22% reached by the surface relaxation of thin film, implying that the magnetic configuration change from AFM to FM at the thin film surface is originated in rather complex surface effects beyond the structural relaxation. The FM preference of thin film is predicted to fast suppress as the film thickness incre...

We considered the diffusion behavior which occurred in the initial stages of thin film deposition for the fabrication of a tunneling magneto-resistance (TMR) junction with the use of the density functional theory (DFT). An Al adatom deposited on the Co (111) substrate had the most stable configuration when it was adsorbed on the hcp site and the energy barrier for the diffusion to the neighboring fcc or hcp site was sufficiently low for the Al adatom to move freely. The energy barrier for the Co on the Co substrate was approximately 1.6 times higher than that for the case of Al on a Co substrate. The energies for the step down (step energy barrier) of an adatom from the top of the adatom trimer were estimated as 0.54 eV and 1.09 eV for Al/Al trimer/Co and Co/Co trimer/Co, respectively.

A Comment on the Letter by Hanchul Kim and James R. Chelikowsky, Phys. Rev. Lett. 77, 1063 (1996). The authors of the Letter offer a Reply.