Ge(001) as a template for long-range assembly of π-stacked coronene rows

The adsorption of coronene molecules (C(24)H(12)) on the Ge(001) surface has been studied by means of scanning tunnelling microscopy (STM). Upon room temperature deposition, the coronene molecules adsorb in an upright geometry forming compact layers patterned in rows for coverages of one monolayer and less, being the only example investigated so far in which a pure aromatic hydrocarbon forms a well-ordered monolayer on a non-passivated semiconductor surface. At half monolayer, the molecular rows consist of long chains of π-stacked molecules and the distance between molecular planes is 8 ?. This configuration is maintained upon cooling the system below the transition temperature of Ge(001) (~220 K), but the molecular layer experiences also a transition from rows perpendicular to rows parallel to the Ge dimer rows. We interpret our observations in terms of a weak bonging between molecules and substrate, which facilitates the formation of large ordered domains of molecules, revealing Ge(001) as an ideal template for the growth of this and other aromatic hydrocarbons.     

Bidentate Surface Structures of Glycylglycine on Si(111)7×7 by High-Resolution Scanning Tunneling Microscopy: Site-Specific Adsorption via N-H and O-H or Double N-H Dissociation

The early adsorption stage of glycylglycine on Si(111)7×7 surface has been studied by scanning tunneling microscopy (STM). Filled-state imaging shows that glycylglycine adsorbs dissociatively in a bidentate fashion on two adjacent Si adatoms across a dimer wall or an adatom-restatom pair, with the dissociated H atoms on neighboring restatoms. The present STM result validates our hypothesis that both bidentate configurations involving N-H and O-H dissociation and double N-H dissociation are equally probable. Our STM results further show that the relative surface concentrations of the five bidentate configurations follow a specific ordering. This suggests that N-H dissociation at a center adatom site would likely be followed by N-H dissociation at an adjacent restatom, while N-H dissociation at a corner adatom site would be succeeded by O-H dissociation at an adatom across the dimer wall. Evidently, the strong bidentate interactions also inhibit surface diffusion of the adsorbed glycylglycine fragment, and the adsorption apparently follows random sequential adsorption statistics. The random nature of adsorption is also supported by the similar relative occupancies of the center adatom and corner adatom sites, indicating that the relative reactivities of these adatom sites do not play a significant role. Our DFT computational study shows that all three bidentate (Si-)NHCH(2)CONHCH(2)COO(-Si) adatom-adatom configurations (center-center, corner-corner, center-corner) have similar adsorption energies for a double adatom-adatom pair across the dimer wall, while the (Si-)NHCH(2)CON(-Si)CH(2)COOH bidentate adatom-restatom configuration is energetically favorable. The free -CONH- and -COOH groups remaining on the respective bidentate adstructures could facilitate adsorption of the second adlayer through the formation of hydrogen bonding.     

Dimer pinning and the assignment of semiconductor-adsorbate surface structures

It has been observed in scanning tunneling microscopy (STM) that the adsorption of molecules on the (001) surface of a Group IV semiconductor can lead to an asymmetric ordering of the dimers immediately adjacent to the adsorbate. This so-called pinning may occur along the dimer row on only one, or both sides of the adsorbate. Here we present a straightforward methodology for predicting such pinning and illustrate this approach for several different adsorbate structures on the Si(001) surface. This approach extends earlier work by including the effects of coupling across the adsorbate as well as the nearest-neighbor interactions between the chemisorbed dimer and its adjacent dimers. The results are shown to be in excellent agreement with the room temperature experimental STM data. The examples also show how this approach can serve as a powerful tool for discriminating between alternative possible adsorbate structures on a dimerized semiconductor (001) surface, especially in cases of molecular adsorption where the STM measurements provide insufficient details of the underlying atomic structure.     

Electronic effects induced by single hydrogen atoms on the Ge(001) surface

The properties of an isolated dangling bond formed by the chemisorption of a single hydrogen atom on a dimer of the Ge(001) surface are investigated by first-principles density functional theory (DFT) calculations, and scanning tunneling microscopy (STM) measurements. Two stable atomic configurations of the Ge-Ge-H hemihydride with respect to the neighboring bare Ge-Ge dimers are predicted by DFT. For both configurations, the unpaired electron of the HGe(001) system is found to be delocalized over the surface, rendering the isolated dangling bond of the hemihydride unoccupied. However, local surface charge accumulation, such as may occur during STM imaging, leads to the localization of two electrons onto the hemihydride dangling bond. The calculated surface densities of states for one of the charged Ge-Ge-H hemihydride configurations are found to be in good agreement with atomic-resolution STM measurements on n-type Ge(001). Comparison with a Si-Si-H hemihydride of the Si(001) surface shows similarities in structural properties, but substantial differences in electronic properties.     

Complex Surface Chemistry of an Otherwise Inert Solvent Molecule: Tetrahydrofuran on Si(001)

The reaction of tetrahydrofuran (THF), an otherwise inert solvent molecule, on Si(001) was experimentally studied in ultra‐high vacuum. Using scanning tunneling microscopy (STM) and photoelectron spectroscopy at variable temperature, we could both isolate a datively bound intermediate state of THF on Si(001), as well as the final configuration that bridges two dimer rows of the Si(001) surface after ether cleavage. The latter configuration implies splitting of the O?C bond, which is typically kinetically suppressed. THF thus exhibits a hitherto unknown reactivity on Si(001).     

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.     

Double dative bond configuration: pyrimidine on Ge(100)

The adsorption of pyrimidine onto Ge(100) surfaces has been investigated using real-time scanning tunneling microscopy (STM), temperature-programmed desorption (TPD), and density-functional theory (DFT) calculations. Our results show that the adsorbed pyrimidine molecules are tilted about 40 degrees with respect to the Ge surface, and through a Lewis acid-base reaction form bridges between the down-Ge atoms of neighboring Ge dimer rows by double Ge-N dative bonding without loss of aromaticity. For coverages of pyrimidine up to 0.25 ML, a well-ordered c(4x2) structure results from states that appear in STM micrographs as oval-shaped protrusions, which correspond to pyrimidine molecules datively adsorbed on every other dimer. However, above 0.25 ML, the oval-shaped protrusions gradually change into brighter zigzag lines. At 0.50 ML, a p(2x2) structure results from the states that appear in STM as zigzag lines. The zigzag lines are formed by the attachment of pyrimidine molecules to the down-Ge atoms of every Ge dimer. However, the unstable p(2x2) structure eventually reconstructs into a c(4x2) structure due to steric hindrance between the adsorbed pyrimidine molecules after stopping the exposure of pyrimidine to the surface.     

Adsorption of phenylacetylene on Si(100)-2 x 1: kinetics and structure of the adlayer

Direct adsorption of phenylacetylene on clean silicon surface Si(100)-2 x 1 is studied in ultrahigh vacuum (UHV). The combination of scanning tunnel microscopy (STM) and surface differential reflectance spectroscopy (SDRS) with Monte Carlo calculations are put together to draw a realistic kinetic model of the evolution of the surface coverage as a function of the molecular exposure. STM images of weakly covered surfaces provide evidence of two very distinct adsorption geometries for phenylacetylene, with slightly different initial sticking probabilities. One configuration is detected with STM as a bright spot that occupies two dangling bonds of a single dimer, whereas the other configuration occupies three dangling bonds of adjacent dimers. These data are used to implement a Monte Carlo model which further serves to design an accurate kinetic model. The resulting evolution toward saturation is compared to the optical data from surface differential reflectance spectroscopy (SDRS). SDRS is an in situ technique that monitors the exact proportion of affected adsorption sites and therefore gives access to the surface coverage which is evaluated at 0.65. We investigate the effect of surface temperature on this adsorption mechanism and show that it has no major effect either on kinetics or on structure, unless it passes the threshold of dissociation measured at ca. 200 degrees C. This offers a comprehensive image of the whole adsorption process of phenylacetylene from initial up to complete saturation.     

Controlled fabrication of 1D molecular lines across the dimer rows on the Si(100)-(2 x 1)-H surface through the radical chain reaction

Current interest in the fabrication of organic nanostructures on silicon surface is focused on the self-directed growth of 1D molecular lines with predefined position, structure, composition, and the length on the H-terminated Si(100)-(2 x 1) surface. To date, no studies have succeeded in growing the molecular line across the dimer rows on Si(100)-(2 x 1)-H, which is highly desirable. Using scanning tunneling microscopy (STM), we studied a new molecular system (allyl mercaptan, CH2=CH-CH2-SH) that undergoes chain reaction across the dimer row on the Si(100)-(2 x 1)-H surface at 300 K and produces covalently bonded 1D molecular lines. In combination with the previous findings of chain reaction along the rows, the present observations of self-directed growth of 1D molecular lines across the dimer rows on the Si(100)-(2 x 1)-H surface provide a means to connect any two points (through molecular lines) on a 2D surface.     

The chemisorption of coronene on Si(001)-2 x 1

Coronene (C24H12) adsorption on the clean Si(001)-2 x 1 surface was investigated by scanning tunneling microscopy and by density-functional calculations. The coronene adsorbed randomly at 25 degrees C on the surface and did not form two-dimensional islands. The scanning tunneling microscopy measurements revealed three adsorption sites for the coronene molecule on the Si(001) surface at low coverage. The major adsorption configuration involves coronene bonding to four underlying Si atoms spaced two lattice spacings apart in a dimer row. The two minor adsorption configurations involve asymmetrical bonding of a coronene molecule between Si dimer rows and form surface species with a mirror plane symmetry to their chiral neighbor species. The two minor bonding arrangements are stabilized by a type-C defect on the Si(001) surface.     

Self-induced 1-D molecular chain growth of thiophene on Ge(100)

The adsorption of thiophene on Ge(100) has been studied using scanning tunneling microscopy (STM), high-resolution core-level photoemission spectroscopy (HRPES), and density functional theory (DFT) calculations. Until now, thiophene is known to react with the Ge(100) dimer through a [4 + 2] cycloaddition reaction at room temperature, similar to the case of thiophene on Si(100). However, we found that thiophene has two adsorption geometries on Ge(100) at room temperature, such as a kinetically favorable Ge-S dative bonding configuration and a thermodynamically stable [4 + 2] cycloaddition adduct. Moreover, our STM results show that under 0.25 ML thiophene molecules preferentially produce one-dimensional molecular chain structures on Ge(100) via the Ge-S dative bonding configuration.     

Theoretical study of the reaction of acrylonitrile on Si(001)

Two recent experiments for adsorbed acrylonitrile on the Si(001) surface reported different adsorption structures at 110 and 300 K. We investigate the reaction of acrylonitrile on Si(001) by first-principles density-functional calculations. We find that the so-called [4+2] structure in which acrylonitrile resides between two dimer rows is not only thermodynamically favored over other structural models but also easily formed via a precursor where the N atom of acrylonitrile is attached to the down atom of the Si dimer. The additional initial-state theory calculation for the C 1s core levels of adsorbed acrylonitrile provides an interpretation for the observed low- and room-temperature adsorption configurations in terms of the precursor and [4+2] structures, respectively.     

Purely site-specific chemisorption and conformation of trimethylamine on Si(100)c(4 x 2)

One of the fundamental points of interest on the Si(100) surface is how the spatial localization of electron density on the buckled silicon dimer controls the site-specific reaction toward different Lewis acid and Lewis base molecules. We have investigated the adsorption of trimethylamine (TMA) on Si(100)c(4x2) using scanning tunneling microscopy (STM) at 80 K. The adsorbed TMA appears as a triangle-shaped bright protrusion in the occupied-state STM image. The triangle-shaped protrusion is ascribed to three methyl groups in the adsorbed TMA. The center of the protrusion is located on the down atom site, which indicates that the adsorption of TMA occurs only on the down dimer atom. Thus, TMA adsorption on Si(100)c(4x2) is found to be purely site-specific on the down dimer atom and can be categorized in Lewis acid-base reaction.     

Physisorption of N2, O2, and CO on fully oxidized TiO2(110)

Physisorption of N(2), O(2), and CO was studied on fully oxidized TiO(2)(110) using beam reflection and temperature-programmed desorption (TPD) techniques. Sticking coefficients for all three molecules are nearly equal (0.75 +/- 0.05) and approximately independent of coverage suggesting that adsorption occurs via a precursor-mediated mechanism. Excluding multilayer coverages, the TPD spectra for all three adsorbates exhibit three distinct coverage regimes that can be interpreted in accord with previous theoretical studies of N(2) adsorption. At low coverages (0-0.5 N(2)/Ti(4+)), N(2) molecules bind head-on to five-coordinated Ti(4+) ions. The adsorption occurs preferentially on the Ti(4+) sites that do not have neighboring adsorbates. This arrangement minimizes the repulsive interactions between the adsorbed molecules along the Ti(4+) rows resulting in a relatively small shift of the TPD peak (105 --> 90 K) with increasing coverage. At higher N(2) coverages (0.5-1.0 N(2)/Ti(4+)) the nearest-neighbor Ti(4+) sites become occupied. The close proximity of the adsorbates results in strong repulsion thus giving rise to a significant shift of the TPD leading edges (90 --> 45 K) with increasing coverage. For N(2)/Ti(4+) > 1, an additional low-temperature peak (approximately 43 K) is present and is ascribed to N(2) adsorption on bridge-bonded oxygen rows. The results for O(2) and CO are qualitatively similar. The repulsive adsorbate-adsorbate interactions are largest for CO, most likely due to alignment of CO dipole moments. The coverage-dependent binding energies of O(2), N(2), and CO are determined by inverting TPD profiles.     

STM study of glycine on TiO2(110) single crystal surfaces

The adsorption of glycine (NH2CH2COOH) was examined by scanning tunneling microscopy (STM) on TiO2(110) surfaces at room temperature. A (2x1) ordered overlayer was observed on the TiO2(110)-(1x1) surface. The adsorption of acetic acid and propanoic acid was also investigated on this surface and their STM images were quite similar to that of glycine. Since acetate and propanoate are formed by dissociative adsorption of these acids on TiO2(110), it is proposed that glycine adsorbs in the same way to form a glycinate. The amino group in the glycinate adlayer structurally analogous to those formed from aliphatic carboxylic acids would be extended away from the surface and potentially free to participate in additional reactions. The underlying structure of the TiO2 surface is important in determining the structure of the glycinate adlayer; no ordering of these adsorbates was observed on the TiO2(110)-(1x2) surface.     

H atom adsorption and diffusion on Si(110)-(1×1) and (2×1) surfaces

We present a periodic density-functional study of hydrogen adsorption and diffusion on the Si(110)-(1×1) and (2×1) surfaces, and identify a local reconstruction that stabilizes the clean Si(110)-(1×1) by 0.51 eV. Hydrogen saturates the dangling bonds of surface Si atoms on both reconstructions and the different structures can be identified from their simulated scanning tunneling microscopy/current image tunneling spectroscopy (STM/CITS) images. Hydrogen diffusion on both reconstructions will proceed preferentially along zigzag rows, in between two adjacent rows. The mobility of the hydrogen atom is higher on the (2×1) reconstruction. Diffusion of a hydrogen vacancy on a monohydride Si(110) surface will proceed along one zigzag row and is slightly more difficult (0.2 eV and 0.6 eV on (1×1) and (2×1), respectively) than hydrogen atom diffusion on the clean surface.     

Study by scanning tunneling microscopy of hydrogen adsorption and desorption on Si111 7 x 7 at room temperature and at high temperature

An overview is given on the use of scanning tunneling microscopy (STM) for investigation of the adsorption of hydrogen on Si(111)7 x 7 both at room temperature and at elevated temperature to finally obtain a hydrogen-saturated surface of Si(111). The initial stages are characterized by high reactivity of Si adatoms of the 7 x 7 structure. After adsorption of hydrogen on the more reactive sites in the beginning of the adsorption experiments a regular pattern, which is different for room and elevated temperature, is observed for the less reactive sites. In agreement with previous work, local 1 x 1 periodicity of the rest atom layer and the presence of di- and trihydride clusters is observed for hydrogen-saturated surface. STM has also been used to characterize surfaces from which the hydrogen atoms have been removed by thermal desorption. Finally, tip-induced desorption by large positive sample-bias voltages and by increasing the tunneling current will be described.     

Origin of nonlocal interactions in adsorption of polar molecules on Si(001)-2 x 1

Using density functional theory slab calculations, we have investigated (i) the origin of nonlocal interactions occurring in the adsorption of small polar molecules (H2O,NH3,CH3OH,CH3NH2) on the clean Si(001)-2 x 1 surface and (ii) the nonlocal effects on two-dimensional arrangement of adsorbates. Our results show the adsorption properties are significantly altered in the presence of adsorbates on an adjacent dimer along a row. We have identified that the coverage dependent behavior arises from a combination of (i) surface polarization change, (ii) adsorbate-induced charge delocalization, (iii) adsorbate-adsorbate repulsion, and (iv) hydrogen bonding. The nucleophilic-electrophilic molecular adsorption involves charge delocalization to neighboring dimers along a row, which in turn undermines molecular adsorption on the neighboring dimers. Nonlocal effects associated with polar interactions with neighboring dimers and adsorbates vary with adsorption system. While such polar interactions are unimportant in CH3OH adsorption, hydrogen bonding and adsorbate-adsorbate repulsion play an important role in determining the adsorption structures of H2O and NH3CH3NH2, respectively. In addition, the electrostatic attraction with the buckled-up Si atoms of adjacent dimers contributes to stabilization of H2O, NH3, and CH3NH2 adsorption. We also discuss kinetic effects on two-dimensional ordering of adsorbates, in conjunction with surface phase transition and adsorption-dissociation rates.     

Surface Chemistry of tert‐Butylphosphine (TBP) on Si(001) in the Nucleation Phase of Thin‐Film Growth

We combine density functional theory calculations and scanning tunneling microscopy investigations to identify the relevant chemical species and reactions in the nucleation phase of chemical vapor deposition. tert‐Butylphosphine (TBP) was deposited on a silicon substrate under conditions typical for surface functionalization and growth of semiconductor materials. On the activated hydrogen‐covered surface H/Si(001) it forms a strong covalent P?Si bond without loss of the tert‐butyl group. Calculations show that site preference for multiple adsorption of TBP is influenced by steric repulsion of the adsorbate's bulky substituent. STM imaging furthermore revealed an anisotropic distribution of TBP with a preference for adsorption perpendicular to the surface dimer rows. The adsorption patterns found can be understood by a mechanism invoking stabilization of surface hydrogen vacancies through electron donation by an adsorbate. The now improved understanding of nucleation in thin‐film growth may help to optimize molecular precursors and experimental conditions and will ultimately lead to higher quality materials.     

Density functional theory study of one-dimensional growth of styrene on the hydrogen-terminated Si(001)-(3 x 1) surface

Recent experimental work has shown that the addition of styrene molecules to hydrogen-terminated Si(001) surfaces leads to the formation of one-dimensional molecular structures through a radical-initiated surface chain reaction mechanism. These nanometric structures are observed to be directed parallel to the dimer rows on the H-Si(001)-(2 x 1) surface and perpendicular to the same rows on H-Si(001)-(3 x 1). Using periodic density functional theory (DFT) calculations, we have studied the initial steps of the radical chain mechanism on the H-Si(001)-(3 x 1) surface and compared them to analogous results for H-Si(001)-(2 x 1). On the H-Si(001)-(3 x 1) surface, one of the crucial steps of the surface chain reaction, namely, the abstraction of a H atom from a nearby surface hydride unit, is found to have a somewhat smaller activation energy in the direction perpendicular to the dimer rows (H abstraction from the nearest dihydride site) than along the rows (H abstraction from a neighboring dimer). Additionally, due to the steric repulsion between the styrene molecules and the SiH2 subunits, growth along the dimer rows is not thermodynamically favorable on the (3 x 1) surface. On the other hand, due to the absence of the SiH2 subunits, growth parallel to the Si dimer rows becomes favored on the H-Si(001)-(2 x 1) surface.