Self-assembled molecular corrals on a semiconductor surface

Nano-corrals for capturing surface electrons are of interest in molecular electronics. Here we show that haloalkane molecules, e.g., 1-chlorododecane, physisorbed on Si(1 1 1)-(7 × 7) self-assemble to form dimers stable to 100 °C which corral silicon adatoms. Corral size is shown to be governed by the haloalkane chain-length. Spectroscopic and theoretical evidence shows that the haloalkane dimer induces electron transfer to the corralled adatom, shifting its energy levels by ∼1 eV. Isolation of a labile pre-cursor points to a model for corral formation which combines mobility with immobility; monomers diffusing in a mobile vertical state meet and convert to the immobile horizontal dimers constituting the corrals.     

DFT study on dissociative adsorption of SiH4 and GeH4 on SiGe(1 0 0)-2 × 1 surface

SiH₄ and GeH₄ dissociative adsorptions on a buckled SiGe(1 0 0)-2 × 1 surface have been analyzed using density functional theory (DFT) at the B3LYP level. The Ge alloying in the Si(1 0 0)-2 × 1 surface affects the dimer buckling and its surface reactivity. Systematic Ge influences on the reaction energetics are found in SiH₄ and GeH₄ reactions with four dimers of Si^∗-Si, Ge^∗-Si, Ge^∗-Ge, and Si^∗-Ge (∗ denotes the protruded atom). On a half H-covered surface, the energy barriers for silane and germane adsorption are higher than those on the pristine surface. The energy barrier for silane adsorption is higher than the corresponding barrier for germane adsorption. Rate constants are also calculated using the transition-state theory. We conclude that the SiGe surface reactivity in adsorption reaction depends on the Ge presence in dimer form. If the surface Ge is present in form of Ge^∗-Ge, the surface reactivity decreases as the Ge^∗-Ge content increases. If the surface Ge prefers to be in form of Ge^∗-Si at low Ge contents, the surface reactivity increases first, then decreases at high Ge surface contents when Ge^∗-Ge prevails. The calculated rate constant ratio of GeH₄ adsorption on Si^∗-Si over Ge^∗-Ge at 650 °C is 2.1, which agrees with the experimental ratio of GeH₄ adsorption probability on Si(1 0 0) over Si(1 0 0) covered by one monolayer Ge. The experimental ratio is 1.7 measured through supersonic molecular beam techniques. This consistency between calculation and experimental results supports that one monolayer of Ge on Si(1 0 0) exists in form of Ge^∗-Ge dimer.     

Adsorption of 2-butyne on Si(0 0 1) at room temperature: A valence band photoemission study

We present an angle resolved ultraviolet photoemission spectroscopy study of the adsorption of 2-butyne (CH₃-CC-CH₃) on Si(0 0 1)-2 × 1 at room temperature. We recorded valence band photoemission spectra for two azimuthal positions of a vicinal silicon surface, where all the rows formed by the surface silicon dimers are parallel. The photoemission symmetry selection rules allow the determination of the orientation of the molecular orbitals. The photoemission signal of the HOMO is enhanced when the electric field is parallel to the dimer rows. This showed that the π orbital left intact after the cyclo-addition reaction of the molecule with one silicon dimer is parallel to the dimer rows. This indicates that each 2-butyne molecule adsorbs on one silicon dimer. In spite of the size of the system and the vicinity of the orbitals, the angle resolved study points out that no dispersion of the electronic bands occurs. Not all the surface dimers are reacted so some disorder still exists on the surface preventing the formation of Bloch states.     

Atomic and electronic structure of Sr/Si(0 0 1)-(2 × 2)

The adsorption of Sr on the Si(0 0 1) surface with the semiantiphase dimer (2 × 2) reconstruction is studied, based upon the ab initio pseudopotential calculations. It is calculated that the semiantiphase dimer (2 × 2) reconstruction (2 dimers per unit cell) is more favorable than the (2 × 1) phase (1 dimer per unit cell) by an energy of about 0.24 eV/dimer. Considering the energetically more stable reconstruction, we have assumed four possible locations for 1/4 monolayer (ML) Sr adsorption on this surface: (i) bridge, (ii) cave, (iii) pedestal, and (iv) valley-bridge. We find that Sr adsorption on the valley-bridge site is energetically more favorable than all other cases studied here. Interestingly, one of the dimers becomes symmetric, but the other one is still asymmetric with the buckling angle reduced from 18° to 14°, when compared with the clean Si(0 0 1)-(2 × 2) surface. The calculated bond length between Sr and Si in the case of valley-bridge adsorption site is 3.05 Å, and in good agreement with other theoretical calculations. We also present and compare the electronic band structures for the clean and covered surfaces as well as the corresponding charge density plots.     

Progressive changes in atomic structure and gap states on Si(0 0 1) by Bi adsorption

From ab initio studies employing the pseudopotential method and the density functional scheme, we report on progressive changes in geometry, electronic states, and atomic orbitals on Si(0 0 1) by adsorption of different amounts of Bi coverage. For the 1/4 ML coverage, uncovered Si dimers retain the characteristic asymmetric (tilted) geometry of the clean Si(0 0 1) surface and the Si dimers underneath the Bi dimer have become symmetric (untilted) and elongated. For this geometry, occupied as well as unoccupied surface states are found to lie in the silicon band gap, both sets originating mainly from the uncovered and tilted silicon dimers. For the 1/2 ML coverage, there are still both occupied and unoccupied surface states in the band gap. The highest occupied state originates from an elaborate mixture of the p_z orbital at the Si and Bi dimer atoms, and the lowest unoccupied state has a ppσ* antibonding character derived from the Bi dimer atoms. For 1 ML coverage, there are no surface states in the fundamental bulk band gap. The highest occupied and the lowest unoccupied states, lying close to band edges, show a linear combination of the p_z orbitals and ppσ* antibonding orbital characters, respectively, derived from the Bi dimer atoms.     

Adsorption and reactions of HN3 on Si(1 0 0)-2 × 1: A computational study

We have studied the adsorption and decomposition of HN₃ on Si(1 0 0)-2 × 1 surface using the hybrid density functional B3LYP method and effective core potential basis, LanL2DZ, with Si₁₅H₁₆ as a double dimer surface model for cluster calculations. The result shows that the barriers for the dissociative adsorption of HN₃ forming HN(a) + N₂(g) are quite low by stepwise dissociation processes occurring either on a dimer or across the dimers. The low activation energies are consistent with previous experimental observations that the molecularly adsorbed HN₃(a) can undergo decomposition producing HN(a) at low surface temperatures. On the other hand, the predicted activation energies for the N₃(a) + H(a) formation processes are all relatively higher. These results also explain the absence of the N₃(a) species in HREELS measurements following each annealing experiment. Several selected reaction paths were also confirmed with slab model calculations using an optimization approach coupling the energy and gradient calculations by the slab model with the geometrical optimization using Berny algorithm.In addition, the adsorbate effect was examined for the end-on and side-on molecular configurations. For the side-on adsorption configuration, all possible combinations with 1-4 adsorbates can exist on the four surface Si sites of the double dimers, with adsorption energies lying closely to the multiples of that of a single side-on adsorbate (LM2); i.e., adsorption energies are nearly additive. Interestingly, for the end-on adsorption, only 1 and 2 HN₃ molecules can adsorb on a dimer due to the presence of the negative charges on the remaining Si sites in the neighboring dimer. For the two end-on adsorbates on the same dimer, the total adsorption energy is close to two times that of HN₃(a) or LM1. For the mixed end-on/side-on configurations, only one of each type can co-exist on a single dimer pair (Si₁-Si₂ or Si₃-Si₄) sites with adsorption energy close to the sum of those of one end-on and one side-on adsorbate. Finally, the predicted reaction routes and vibrational frequencies showed good agreement with previous experimental results. The stabilities of many ad-species involved in these reactions with end-on and/or side-on configurations have been predicted together with the transition states connecting those species.     

Diffusion of Pb adatom and ad-dimer on Si(1 0 0) from ab initio studies

The diffusion pathways of Pb adatoms and ad-dimers on Si(1 0 0) are investigated by first-principles calculations. Pb adatoms are found to diffuse on top of the Si(1 0 0) dimer row with an energy barrier of 0.31 eV. However, Pb dimers are energetically more stable. Pb dimers on top of the dimer row have a high energy barrier (0.95 eV) to rotate from the lowest energy configuration to the orientation parallel to the underlying Si(1 0 0) dimer row. Once the ad-dimer is oriented parallel to Si(1 0 0) dimer row, they can diffuse along the dimer row with an energy barrier of only 0.32 eV.     

An ab initio-based approach to phase diagram calculations for GaAs(0 0 1)-(2 × 4)γ surfaces

Surface phase diagram of recently proposed GaAs(0 0 1)-(2 × 4)γ is systematically investigated by using our ab initio-based approach. We focus on the (4 × 7) domain consisting of c(4 × 4)-like and (2 × 4)-like regions to clarify surface dimer constituents as functions of temperature T and As (As₂ and As₄) pressure p_As by comparing chemical potentials of surface dimers in the vapor phase with that on the surface. The calculated results under As₄ imply that Ga dimers in the c(4 × 4)-like region tend to become stable with increase of temperature and appear at the conventional growth condition such as T ∼ 800 K and p_As ∼ 10⁻⁶ Torr, while the (2 × 4)-like region favors As dimers. This is consistent with temperature dependence of change in surface dimer constituents on the c(4 × 4) and (2 × 4)β2 clarified in our previous study. Furthermore, the surface phase transition from the c(4 × 4) to (2 × 4)β2 via (2 × 4)γ is discussed on the basis of the phase diagram obtained in this study.     

Simulations of iodine adsorbed Ge(0 0 1) surface and its STM images

A layer of iodine at Ge(0 0 1) surface develops an ordered structure of iodine atoms bound to Ge dimers. Here are discussed atomic structures of Ge(0 0 1) surface covered by 0.25 monolayer of iodine. The p(2×4), p(2×2), c(2×4) and p(1×4) surface structures are found in calculations. The structure with two iodine atoms of the dissociated I₂ molecule adsorbed at both ends of the same germanium dimer is found to be energetically favourable over iodine adsorption at neighbouring dimers. Simulated STM images of the obtained surface structures are presented and compared with experimental data.     

First self-assembly study of large π-conjugated corrole dimers on solid substrates

Our study focus on β,β′-doubly linked corrole dimers (CDs) on mica and Au(1 1 1) surface using samples prepared by the synthetic method described by Osuka group appeared on recent publication [S. Hiroto, K. Furukawa, H. Shinokubo, A. Osuka, J. Am. Chem. Soc. 128 (2006) 12380]. Atomic force microscopy (AFM) and scanning tunneling microscopy (STM) were used to investigate the self-assembled structure of corrole dimers adsorbed on mica and Au(1 1 1) surfaces respectively at room temperature in air. The CDs adopt a dissimilar adsorption modality due to the different surface free energy of the different substrates. These types of molecular layers provide a useful platform for the study of surface and interface phenomena outside a vacuum system. It is potentially useful for practical fabrication of molecular devices because of the simplicity of the sample preparation and the stability of the interface in ambient conditions.     

Surface etching induced by Ce silicide formation on Si(1 0 0)

We investigate the temperature-dependent surface etching process induced by Ce silicide on Si(1 0 0) using scanning tunneling microscopy and X-ray photoelectron spectroscopy. We found that step edges on the Si(1 0 0) surface are gradually roughened due to the formation of Ce silicide as a function of substrate temperature. Unlike the Si(1 1 1) surface, however, terrace etching also occurs in addition to step roughening at 500 °C. Moreover, we found that Si(1 0 0) dimers are released and formed dimer vacancy lines because bulk diffusion of Ce silicide into Si(1 0 0) surface occurs the defect-induced strain at higher temperature (∼600 °C).     

Self-assembly of 2,6-dimethylpyridine on Cu(1 1 0) directed by weak hydrogen bonding

Sequential stages of formation of a self-assembled monolayer of flat-lying 2,6-dimethylpyridine molecules on a single crystal Cu(1 1 0) surface have been observed by low-temperature scanning tunneling microscopy (LT-STM). At an adsorption temperature of 10 K, all of the molecules are randomly distributed at low coverage upon adsorption. The isolated molecules align their molecular axes parallel to the 〈0 0 1〉 azimuth of the Cu lattice. The nitrogen atom in the molecule is located at the four-fold hollow site. Upon annealing to 100 K, the molecules associate to form head-to-head dimers. The dimer units involve a pair of weak hydrogen bonds between methyl group-hydrogen atoms and N moieties on adjacent molecules, forming a core structure for further growth. In a later stage of self-assembly, single head-to-tail weak hydrogen bonds between ring C-H bonds and N moieties form in chains on the periphery of the central cores, leading to larger domains with a c(6 × 2) overlayer structure.     

Ab initio study of platinum induced reconstructions on Ge(001)-(1×2) surface with dimerization

We present first principle total energy calculation of Pt induced reconstructions on Ge(001)-(1×2) surface with dimerization. Study was undertaken using localized orbitals basis set DFT using SIESTA to compare pure Ge dimerized Ge(001)-(1×2) surface with 0.5 and 1.0 Pt covered dimerized Ge(001)-(1×2) surface with the possibility of homo (Ge-Ge and Pt-Pt) and hetro (Pt-Ge) dimers. From total energy calculation results we calculated dimer bond lengths, buckling angles and formation energy of dimers on Ge(001)-(1×2) surface. By calculating the formation energy of different configurations we find that Ge-Ge buckled dimerized surface has least (−1.23 eV/dimer) and Pt-Pt symmetric dimerized surface has largest (+0.09 eV/dimer) formation energy with respect to unreconstructed surface. We further calculated the electronic DOS and band structure of Ge dimerized as well as Pt dimerized surface to see the change in semiconducting behavior on dimerization. By comparing the DOS and electronic band structure of homo Ge dimerized surface, we found metallicity of Ge(001)-(1×2) surface results from dimer formation. Also by comparing the electronic band structure of homo Ge dimerized surface with unreconstructed surface we find that less number of bands crossing the Fermi level which is perhaps due to the saturation of one dangling bond per Ge surface atom. By introducing Pt at 0.5 and 1.0 coverage in place of Ge, except for homo Pt buckled dimerized surface having 1.0 coverage of Pt, we find in all other cases increase in number of bands are crossing the Fermi level, indicating strong metallic behavior of Ge(001)-(1×2) surface.     

Pd diffusion on MgO(1 0 0): The role of defects and small cluster mobility

Density functional theory is used to explore the energy landscape of Pd atoms adsorbed on the terrace of MgO(1 0 0) and at oxygen vacancy sites. Saddle point finding methods reveal that small Pd clusters diffuse on the terrace in interesting ways. The monomer and dimer diffuse via single atom hops between oxygen sites with barriers of 0.34 eV and 0.43 eV respectively. The trimer and tetramer, however, form 3D clusters by overcoming a 2D-3D transition barrier of less than 60 meV. The trimer diffuses along the surface either by a walking or flipping motion, with comparable barriers of ca. 0.5 eV. The tetramer rolls along the terrace with a lower barrier of 0.42 eV. Soft rotational modes at the saddle point lead to an anomalously high prefactor of 1.3 × 10¹⁴ s⁻¹ for tetramer diffusion. This prefactor is two order of magnitude higher than for monomer diffusion, making the tetramer the fastest diffusing species on the terrace at all temperatures for which diffusion is active (above 200 K). Neutral oxygen vacancy sites are found to bind Pd monomers with a 2.63 eV stronger binding energy than the terrace. A second Pd atom, however, binds to this trapped monomer with a smaller energy of 0.56 eV, so that dimers at defects dissociate on a time scale of milliseconds at room temperature. Larger clusters bind more strongly at defects. Trimers and tetramers dissociate from monomer-bound-defects at elevated temperatures of ca. 600 K. These species are also mobile on the terrace, suggesting they are important for the ripening observed at ?600 K during Pd vapor deposition on MgO(1 0 0) by Haas et al. [G. Haas, A. Menck, H. Brune, J.V. Barth, J.A. Venables, K. Kern, Phys. Rev. B 61 (2000) 11105].     

Chemisorption of 4-(4-amino-phenylazo) benzoic acid molecule on the Si(0 0 1)-(4 × 2) surface

Structural and electronic properties of self-assembled monolayer with 4-(4-amino-phenylazo) benzoic acid (APABA) on the Si(0 0 1)-(4 × 2) surface are investigated by ab initio calculation based on density functional theory. For the APABA chemisorption on the silicon surface, we have assumed two different binding sites: (i) amino group of molecule and (ii) carboxyl group of molecule. Considering amino-site, we have assumed two possible models for the chemisorption of molecules on the Si(0 0 1)-(4 × 2) surface: (i) an intrarow position between two neighboring Si dimers in the same dimer row (Model I), (ii) on-dimer position (Model II). We have found that Model II is 1.10 eV energetically more favorable than Model I. The Si-N bond length was calculated as 1.85 Å which is in excellent agreement with the sum of the corresponding covalent radii of 1.87 Å. Considering carboxyl-site, we have assumed exactly the same model as mentioned above. Again we have found that Model II is energetically favorable than Model I. The calculated bond lengths for Si-O and O-C are 1.76 and 1.35 Å, respectively.     

Effect of hydrogenation on B/Si(0 0 1)-(1 × 2)

Ab initio calculations, based on pseudopotentials and density functional theory, have been performed to investigate the effect of hydrogenation on the atomic geometries and the energetics of substitutional boron on the generic Si(0 0 1)-(1 × 2) surface. For a single B atom substitution corresponding to 0.5 ML coverage, we have considered two different sites: (i) the mixed Si-B dimer structure and (ii) boron substituting for the second-layer Si to form Si-B back-bond structure, which is energetically more favorable than the mixed Si-B dimer by 0.1 eV/dimer. However, when both of these cases are passivated by hydrogen atoms, the situation is reversed and the Si-B back-bond case becomes 0.1 eV/dimer higher in energy than the mixed Si-B dimer case. For the B incorporation corresponding to 1 ML coverage, among the substitutional cases, 100% interdiffusion into the third layer of Si and 50% interdiffusion into the second layer of Si are energetically similar and more favorable than the other cases that are considered. However, when the surface is passivated with hydrogen, the B atoms energetically prefer to stay at the third layer of the Si substrate.     

Towards hybrid silicon-organic molecular electronics: The stability of acetone on the Si(0 0 1) surface

We present the results of a combined study using scanning tunneling microscopy (STM) and density functional theory (DFT) of the interaction of acetone [(CH₃)₂CO] with the Si(0 0 1) surface. Three distinct adsorbate features were observed using atomic-resolution STM. One of the features appears as a bright protrusion located above a Si-Si dimer, while the other two are asymmetric about the dimer row and involve a second neighboring Si-Si dimer. One of the two asymmetric features has a protrusion located between the two dimers, while the other has a protrusion which is located at the site of a single dimer and exhibits a dimer sized depression on the adjacent dimer. DFT calculations have been performed for two structures; the four-membered ring structure and dissociation structure. Our calculations show that the bright single-dimer sized feature observed in the STM images could be attributed to either of these two calculated structures. However, neither of the two calculated structures can explain the appearance of the two-dimer wide asymmetric features observed in the experiment.     

Adsorption of N@C60 on Si(1 0 0)

The interactions between endohedrally doped N@C₆₀ molecules and the Si(1 0 0) surface have been explored via ab initio total energy calculations. Configurations which have the cage located upon the dimer row bonded to two dimers (r2) and within the dimer trench bonded to four dimers (t4) have been investigated, as these have previously been found to be the most stable for the C₆₀ molecule. We have investigated the differences between the adsorption of the C₆₀ and N@C₆₀ molecules upon the Si(1 0 0) surface and found that there are only minimal differences. Two interesting cases are the r2g and t4d configurations, as they both exhibit differences that are not present in the other configurations. These subtle differences have been explored in-depth. It is shown that the effects on the endohedral nitrogen atom, due to its placement within the fullerene cage, are small. Bader analysis has been used to explore differences between the C₆₀ and N@C₆₀ molecules.     

Irreversible structural transformation of Si(1 1 4)-2 × 1 induced by subsurface carbon

Using scanning tunneling microscopy (STM), it has been found that the reconstruction of Si(1 1 4) is transformed irreversibly from a 2 × 1 structure composed of dimer (D), rebonded atom (R), and tetramer (T) rows (phase A) to a different kind of 2 × 1 structure composed of D, T, and T rows (phase B) by C incorporation. It has been confirmed by high-resolution synchrotron core-level photoemission spectroscopy (PES) that such an irreversible structural transformation is due to stable subsurface C atoms. They induce anisotropic compressive stress on the surface, which results in insertion of Si dimers to an R row to form a T row.     

The effect of controlled ion bombardment on the electronic structure of the Si(0 0 1) surface

We have studied the effects of controlled ion bombardment on the electronic structure of the Si(0 0 1) surface. The surface was exposed to various doses of Ar⁺ ions accelerated towards the surface at 500 eV. X-ray photoelectron spectroscopy (XPS) spectra of the irradiated H-terminated Si(0 0 1) surface reveal the appearance of peaks that are associated with the presence of cleaved Si bonds. Ultraviolet photoelectron spectroscopy (UPS) spectra of the irradiated Si(0 0 1)2 × 1 surface show that the dimer dangling-bond surface state decays monotonically with increasing dose. These results, coupled with previous scanning tunneling microscopy (STM) studies, indicate that the breaking of dimers, and possibly the creation of adatom-like defects, during ion irradiation are responsible for the changes in the electronic structure of the valence band for this surface.