Study of adsorption and decomposition of H2O on Ge(100)

The adsorption and decomposition of water on Ge(100) have been investigated using real-time scanning tunneling microscopy (STM) and density-functional theory (DFT) calculations. The STM results revealed two distinct adsorption features of H2O on Ge(100) corresponding to molecular adsorption and H-OH dissociative adsorption. In the molecular adsorption geometry, H2O molecules are bound to the surface via Ge-O dative bonds between the O atom of H2O and the electrophilic down atom of the Ge dimer. In the dissociative adsorption geometry, the H2O molecule dissociates into H and OH, which bind covalently to a Ge-Ge dimer on Ge(100) in an H-Ge-Ge-OH configuration. The DFT calculations showed that the dissociative adsorption geometry is more stable than the molecular adsorption geometry. This finding is consistent with the STM results, which showed that the dissociative product becomes dominant as the H2O coverage is increased. The simulated STM images agreed very well with the experimental images. In the real-time STM experiments, we also observed a structural transformation of the H2O molecule from the molecular adsorption to the dissociative adsorption geometry.     

Phosphine dissociation and diffusion on Si(001) observed at the atomic scale

A detailed atomic-resolution scanning tunneling microscopy (STM) and density functional theory study of the adsorption, dissociation, and surface diffusion of phosphine (PH(3)) on Si(001) is presented. Adsorbate coverages from approximately 0.01 monolayer to saturation are investigated, and adsorption is performed at room temperature and 120 K. It is shown that PH(3) dissociates upon adsorption to Si(001) at room temperature to produce both PH(2) + H and PH + 2H. These appear in atomic-resolution STM images as features asymmetric-about and centered-upon the dimer rows, respectively. The ratio of PH(2) to PH is a function of both dose rate and temperature, and the dissociation of PH(2) to PH occurs on a time scale of minutes at room temperature. Time-resolved in situ STM observations of these adsorbates show the surface diffusion of PH(2) adsorbates (mediated by its lone pair electrons) and the dissociation of PH(2) to PH. The surface diffusion of PH(2) results in the formation of hemihydride dimers on low-dosed Si(001) surfaces and the ordering of PH molecules along dimer rows at saturation coverages. The observations presented here have important implications for the fabrication of atomic-scale P dopant structures in Si, and the methodology is applicable to other emerging areas of nanotechnology, such as molecular electronics, where unambiguous molecular identification using STM is necessary.     

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.     

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.     

Coverage dependent supramolecular structures: C60:ACA monolayers on Ag(111)

The dependence of supramolecular structure on fractional molecular coverage has been investigated for acridine-9-carboxylic acid (ACA) and the C(60):ACA binary molecular system. The coverage-dependent phase diagram for ACA is first determined from room-temperature STM imaging. At low molecular coverages (theta < 0.4 ML, ML = monolayer), ACA forms a 2-D gas phase. Ordered ACA structures appear with increasing coverage: first a chain structure composed of ACA molecules linked by consecutive O-H...N hydrogen bonds (theta > 0.4 ML), then a dimer structure composed of ACA dimers linked by paired carboxyl-carboxyl hydrogen bonds (theta approximately equal to 1.0 ML). Structures of the C(60):ACA binary system depend on the coverage of predeposited ACA. At intermediate (0.4 ML approximately 0.8 ML) ACA coverages, C(60) deposition results in a hexagonal cooperative structure with the C(60) periodicity nearly 3 times that of the normal C(60) 2-D packing of 1 nm and exists in enantiopure domains. At higher ACA coverages, a C(60) quasi-chain structure is formed in which parallel C(60) chains are spaced by ACA dimer domains. The mechanistic role of the initial ACA phase in the formation of C(60):ACA supramolecular structures is described. Chemically intuitive molecular packing models are presented based on the observed STM images.     

Ab initio surface reaction energetics of SiH4 and Si2H6 on Si(001)-(2 x 2)

First-principles pseudopotential calculations, within a simple dynamically constrained scheme, have been performed to investigate the reaction of 0.25 ML coverage of SiH4 and Si2H6 with the Si(001)-(2 x 2) surface. The silane molecule (SiH4) is adsorbed on to the surface at a number of different sites (on dimer, interrow, or intrarow) with varying barrier heights. Two distinct structures, which are similar in energy, arise from the initial dissociative reaction SiH4-->SiH3(silyl) + H, where the dissociated species are adsorbed either on the same dimer components or on adjacent dimer components. Several further decays of silyl from SiH4 are presented in two separate regimes of high and low ambient hydrogen coverages. The decomposition of silyl can form two different bridging structures: an on top or an intrarow bridging structure in both of the two hydrogen coverage regimes. The disilane molecule (Si2H6) is also adsorbed upon this surface with varying energy barriers, resulting in a dissociation reaction where two SiH3 species are adsorbed on one dimer or in an adjacent dimer configuration. Plausible energy reaction paths for the above models are presented. The stability of the SiH2 species is also discussed.     

Atomic imaging of nucleation of trimethylaluminum on clean and H2O functionalized Ge(100) surfaces

The direct reaction of trimethylaluminum (TMA) on a Ge(100) surface and the effects of monolayer H(2)O pre-dosing were investigated using ultrahigh vacuum techniques, such as scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), and x-ray photoelectron spectroscopy (XPS), and density functional theory (DFT). At room temperature (RT), a saturation TMA dose produced 0.8 monolayers (ML) of semi-ordered species on a Ge(100) surface due to the dissociative chemisorption of TMA. STS confirmed the chemisorption of TMA passivated the bandgap states due to dangling bonds. By annealing the TMA-dosed Ge surface, the STM observed coverage of TMA sites decreased to 0.4 ML at 250?°C, and to 0.15 ML at 450?°C. XPS analysis showed that only carbon content was reduced during annealing, while the Al coverage was maintained at 0.15 ML, consistent with the desorption of methyl (-CH(3)) groups from the TMA adsorbates. Conversely, saturation TMA dosing at RT on the monolayer H(2)O pre-dosed Ge(100) surface followed by annealing at 200?°C formed a layer of Ge-O-Al bonds with an Al coverage a factor of two greater than the TMA only dosed Ge(100), consistent with Ge-OH activation of TMA chemisorption and Ge-H blocking of CH(3) chemisorption. The DFT shows that the reaction of TMA has lower activation energy and is more exothermic on Ge-OH than Ge-H sites. It is proposed that the H(2)O pre-dosing enhances the concentration of adsorbed Al and forms thermally stable Ge-O-Al bonds along the Ge dimer row which could serve as a nearly ideal atomic layer deposition nucleation layer on Ge(100) surface.     

Imaging fibrinogen adsorbed on noble metal surfaces with scanning tunneling microscopy: correlation of images with electron spectroscopy for chemical analysis, secondary ion mass spectrometry, and radiolabeling studies

Fibrinogen adsorption on gold and platinum surfaces has been studied with electron spectroscopy for chemical analysis (ESCA), secondary ion mass spectrometry (SIMS), ¹²⁵I labeling, and scanning tunneling microscopy (STM). Stable images of single molecules have been obtained, but are rare. ESCA, SIMS, and labeling studies confirm that absorbed fibrinogen is present on samples at monolayer and submonolayer coverages even when STM images show only a bare substrate. Imaging is more reproducible at high coverages at which single molecules cannot be resolved. Possible explanations for the failure of STM to observe adsorbed fibrinogen molecules are discussed.     

Bond character of thiophene on Ge(100): Effects of coverage and temperature

We have studied the adsorption and decomposition of thiophene (C4H4S) on Ge(100) using scanning tunneling microscopy (STM), high-resolution core-level photoemission spectroscopy (HRPES), and density functional theory (DFT) calculation. Analysis of S 2p core-level spectra reveals three adsorption geometries, which we assign to a Ge-S dative bonding state, a [4 + 2] cycloaddition bonding state, and a decomposed bonding state (desulfurization reaction product). Furthermore, we found that the number ratio of the three adsorption geometries depended on the molecular coverage and the annealing temperature. At low coverages, the kinetically favorable dative bonding state is initially formed at room temperature. As the molecular coverage increases, thermodynamically stable [4 + 2] cycloaddition reaction products are additionally produced. In addition, we found that as the surface temperature increased, the [4 + 2] cycloaddition reaction product either possibly desorbed as molecular thiophene or decomposed to form a metallocycle-like species (C4H4Ge2) and a sulfide (Ge2S). We systematically elucidate the changes in the bonding states of adsorbed thiophene on Ge(100) according to the thiophene coverage and annealing temperature.     

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.     

Interpretation of high-resolution images of the best-bound wetting layers on Pt(111)

Two interpretations have been proposed of dark triangles observed in scanning tunneling microscopy (STM) images of the best bound, √37×√37-R25.3°, and √39×√39-R16.1° periodic water monolayers on Pt(111). In one, a "Y"-shaped tetramer of water molecules is removed, leaving a vacancy island behind; the other assumes the Y is replaced by a hexagon of H(2)O molecules, amounting to a di-interstitial. Consistent only with the di-interstitial model are thermal desorption and CO coadsorption data, STM line scans, and total energies obtained from density functional theory calculations.     

A scanning tunneling microscopy study of distyrylbenzene on Ag/Ge(111)-(sqr rt of 3 x sqr rt of 3)R30 degrees

The adsorption and self-organized monolayers of trans,trans-distyrylbenzene (tt-DSB) and cis,cis-distyrylbenzene (cc-DSB) on Ag/Ge(111)-(sqr rt of 3 x sqr rt of 3)R30 degrees (Ag/Ge(111)-sqr rt of 3) were studied by low-temperature scanning tunneling microscopy (STM) in ultrahigh vacuum. tt-DSB and cc-DSB overlayers were prepared by vapor deposition at a substrate temperature of 200 K and imaged after the samples were cooled to 100 K. High-resolution images allow identification of the internal structure of individual tt-DSB molecules with three phenyl rings and their molecular arrangements on the Ag/Ge(111)-sqr rt of 3 surface. It is found that the intermolecular distance between two terminal phenyl rings in tt-DSB is about twice the lattice constant of Ag/Ge(111)-sqr rt of 3. Such a lattice match makes Ag/Ge(111)-sqr rt of 3 an ideal substrate for tt-DSB self-organization and the formation of a (3 x 1) overlayer unit cell. The structural model and the molecule registry corresponding to STM images for the adlayers of tt-DSB on Ag/Ge(111)-sqr rt of 3 are proposed and discussed. For cc-DSB adsorption on Ag/Ge(111)-sqr rt of 3, uniform molecular overlayers with two discernible molecular images corresponding to two major types of cc-DSB conformers were observed. The coexistence of multiple conformers and the mismatch of molecular dimension of cc-DSB with the substrate unit cell length limit the growth of large cc-DSB domains.     

Water adsorption on ZnO(1010): from single molecules to partially dissociated monolayers

Static and dynamic density functional calculations have been used to study the structure and energetics of water adsorbed on the main cleavage plane of ZnO. In the single molecule limit we find that molecular adsorption is strongly preferred. The water binding energy increases for higher coverages due to an almost isotropic attractive water-water interaction which leads to clustering and formation of monolayer islands in the low water coverage regime. A thermodynamic analysis further shows that the full water monolayer is clearly the most stable phase until water starts to desorb. The water monolayer is even more stabilized by a partial dissociation of the water molecules, yielding as most stable configuration a (2x1) superstructure where every second water molecule is cleaved. The dissociation barrier for this process is very small which allows for an auto-dissociation of the water molecules even at low temperatures as observed experimentally. Finally we find that the energy cost involved to form [1210]-oriented domain boundaries between (2x1) patches with different orientation is almost negligible which explains the abundance of such domain boundaries in STM images.     

Formation of highly ordered organic monolayers by dative bonding: pyridine on ge(100)

The adsorption of pyridine onto the Ge(100) surface has been studied using both real-time scanning tunneling microscopy (STM) and ab initio pseudopotential density functional calculations. The results show that pyridine molecules adsorb on the electron-deficient down-Ge atoms of the Ge=Ge dimers via Ge-N dative bonding, with the pyridine ring tilted to the surface. The electron-rich up-Ge atoms remaining after adsorption of pyridine induce an asymmetric dimer row, which is mainly reconstructed to the c(4 x 2) structure. At pyridine coverage of 0.25 ML, the adsorbed pyridine molecules form a perfectly ordered monolayer. The entire Ge substrate underlying this organic monolayer rearranges into the c(4 x 2) structure.     

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.     

Structural Transformation of Surface-Confined Porphyrin Networks by Addition of Co Atoms

The self-assembly of a nickel-porphyrin derivative (Ni-DPPyP) containing two pyridyl coordinating sites and two pentyl chains at trans meso positions was studied with scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS) and low energy electron diffraction (LEED) on Au(111). Deposition of Ni-DPPyP onto Au(111) gave rise to a close-packed network for coverages smaller or equal to one monolayer as revealed by STM and LEED. The molecular arrangement of this two-dimensional network is stabilized via hydrogen bonds formed between the pyridyl's nitrogen and hydrogen atoms from the pyrrole groups of neighboring molecules. Subsequent deposition of cobalt atoms onto the close-packed network and post-deposition annealing at 423 K led to the formation of a Co-coordinated hexagonal porous network. As confirmed by XPS measurements, the porous network is stabilized by metal-ligand interactions between one cobalt atom and three pyridyl ligands, each pyridyl ligand coming from a different Ni-DPPyP molecule.     

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.     

Single molecule observations of the adsorption sites of methyl isocyanide on Pt(111) by low-temperature scanning tunneling microscopy

Scanning tunneling microscopy (STM) has been used to directly investigate the local structure of methyl isocyanide (CNCH3) adsorbed on Pt(111). At low coverages, CNCH3 is preferentially adsorbed at on-top sites, in agreement with earlier deductions based on vibrational spectroscopy. When dosed at low coverages at 50 K, the molecules tend to adsorb near other CNCH3 molecules with preferred distances of a and a, where a = 2.78 A is the lattice constant of Pt. Annealing the surface to 120 K, however, results in a more uniform separation of the molecules. At higher coverages, the CNCH3 molecules are observed to occupy both on-top and two-fold bridge sites. On the basis of STM image analysis, CNCH3 forms an ordered layer of (2 x 3) periodicity at 0.33 ML. Additional details on the structures of CNCH3 adsorbed at the on-top and two-fold bridge sites are provided by density functional theory (DFT) calculations. At a coverage that saturates the first layer (0.33 ML), the occupation ratio for the on-top and two-fold bridge bonded CNCH3 is 1:1, which is consistent with the results obtained from the combined use of experimental reflection absorption infrared spectroscopy (RAIRS) data and DFT calculations.     

Adsorption and in situ scanning tunneling microscopy of cysteine on Au(111): Structure, energy, and tunneling contrasts

The amino acid L-cysteine (Cys) adsorbs in highly ordered (3 square root of 3 x 6) R30 degrees lattices on Au(111) electrodes from 50 mM ammonium acetate, pH 4.6. We provide new high-resolution in situ scanning tunneling microscopy (STM) data for the L-Cys adlayer. The data substantiate previous data with higher resolution, now at the submolecular level, where each L-Cys molecule shows a bilobed feature. The high image resolution has warranted a quantum chemical computational effort. The present work offers a density functional study of the geometry optimized adsorption of four L-Cys forms-the molecule, the anion, the neutral radical, and its zwitterion adsorbed a-top-at the bridge and at the threefold hollow site of a planar Au(111) Au12 cluster. This model is crude but enables the inclusion of other effects, particularly the tungsten tip represented as a single or small cluster of W-atoms, and the solvation of the L-Cys surface cluster. The computational data are recast as constant current-height profiles as the most common in situ STM mode. The computations show that the approximately neutral radical, with the carboxyl group pointing toward and the amino group pointing away from the surface, gives the most stable adsorption, with little difference between the a-top and threefold sites. Attractive dipolar interactions screened by a dielectric medium stabilize around a cluster size of six L-Cys entities, as observed experimentally. The computed STM images are different for the different L-Cys forms. Both lateral and vertical dimensions of the radical accord with the observed dimensions, while those of the molecule and anion are significantly more extended. A-top L-Cys radical adsorption further gives a bilobed height profile resembling the observed images, with comparable contributions from sulfur and the amino group. L-Cys radical a-top adsorption therefore emerges as the best representation of L-Cys adsorption on Au(111).     

The mobile proton in polyalanine peptides

Ion mobility measurements have been performed for protonated polyalanine peptides (A10 + H+, A15 + H+, A20 + H+, A25 + H+, and A15NH2 + H+) as a function of temperature using a new high-temperature drift tube. Peaks due to helices and globules were found at room temperature for all peptides, except for A10 + H+ (where only the globule is present). As the temperature is increased, the helix and globule peaks broaden and merge to give a single narrow peak. This indicates that the two conformations interconvert rapidly at elevated temperatures. The positions of the merged peaks show that A15 + H+ and A15NH2 + H+ spend most of their time as globules when heated, while A20 + H+ and A25 + H+ spend most of their time as helices. The helix/globule transitions are almost certainly accompanied by intramolecular proton transfer, and so, these results suggest that the proton becomes mobile (able to migrate freely along the backbone) at around 450 K. The peptides dissociate as the temperature is increased further to give predominantly the bn(+), b(n-1)(+), b(n-2)(+), ... series of fragment ions. There is a correlation between the ease of fragmentation and the time spent in the helical conformation for the An + H+ peptides. Helix formation promotes dissociation because it pools the proton at the C-terminus where it is required for dissociation to give the observed products. In addition to the helix and globule, an antiparallel helical dimer is observed for the larger peptides. The dimer can be collisionally dissociated by injection into the drift tube at elevated kinetic energies.