Tuning the geometry of shape-restricted DNA molecules on the functionalized Si(1 1 1)

Designing a well-defined and stable interface between biomolecules and semiconductor surfaces is of great importance for current and future biosensing and bioelectronic applications. The well-characterized chemistry, stability, and easily tunable electronic properties of silicon substrate make it a practical platform for this type of interface. It has been established in our previous work that a robust, covalent attachment between thiol-DNA molecules of a pre-designed geometrical shape and a modified silicon surface can be achieved. This work focuses on using this binding model and altering the distance between the DNA molecules and silicon surface by strategically placing thiol linkers within the pre-determined geometric design of the rectangularly shaped DNA. The statistical analysis of the height profiles of DNA molecules attached to the surface, as determined by AFM, provides specific insight into how the construction of the DNA molecules affects the binding distance. A comparison between two thiol-DNA molecules with different numbers of thiol groups placed either within the rectangular shape or anchored to the free loop of the same geometric design suggest that the average distance of these molecules to the functionalized silicon surface can be changed by approximately 0.5 nm.     

Adsorption of Ag on Si(1 0 0) surface

The chemisorption of one monolayer Ag atoms on an ideal Si(1 0 0) surface is studied by using the self-consistent tight-binding linear muffin-tin orbital method. The adsorption energies (E_ad) of different sites are calculated. It is found that the adsorbed Ag atoms are more favorable on C site (fourfold site) than on any other sites on Si(1 0 0) surface, the polar covalent bond is formed between Ag atom and surface Si atom, a Ag and Si mixed layer does not exist and does form an abrupt interface at the Ag–Si(1 0 0) interface. This is in agreement with the experiment results. The layer-projected density of states is calculated and compared with that of the clean surface. The charge transfer is also investigated. Comparing with the Au/Si(1 0 0) system, the interaction is weaker between Ag and Si than between Au and Si.     

Thin PTCDA films on Si(0 0 1): 1. Growth mode

We have studied the interface and thin film formation of the organic molecular semiconductor 3,4,9,10 perylene tetracarboxylic dianhydride (PTCDA) on clean and on hydrogen passivated Si(0 0 1) surfaces. The studies were made by means of high resolution X-ray photoelectron spectroscopy (HRXPS), near edge X-ray absorption fine structure (NEXAFS), low energy electron diffraction (LEED), and atomic force microscopy (AFM). On the passivated surface the LEED pattern is somewhat diffuse but reveals that the molecules grow in several ordered domains with equivalent orientations to the substrate. NEXAFS shows that the molecules are lying flat on the substrate. The Si 2p XPS line shape is not affected when the film is deposited so it can be concluded that the interaction at the interface between PTCDA and the substrate is weak. The evolution of the film formation appears to be homogeneous for the first monolayer with a nearly complete coverage of flat lying molecules based on the XPS attenuation. For layer thickness of 0.5-2 monolayers (ML) the molecules start to form islands, attracting the molecules in between, leaving the substrate partly uncovered. For thicker films there is a Stranski-Krastanov growth mode with thick islands and a monolayer thick film in between. For the clean surface the ordering of the film is much lower and angle resolved photoelectron spectroscopy (ARPES) of the molecular orbitals have only a small dependence of the emission angle. NEXAFS shows that the molecules do not lie flat on the surface and also reveal a chemical interaction at the interface.     

Theoretical study on adsorption of Au and hydrated Au cations on clean Si(1 1 1) surface

To model the adsorption of Au⁺ cation in aqueous solution on the semiconductor surface, the interactions of Au⁺ and hydrated Au⁺ cations with clean Si(1 1 1) surface were investigated by using hybrid density functional theory (B3LYP) and Møller-Plesset second-order perturbation (MP2) methods. Si(1 1 1) surface was described with Si₇H₁₁, Si₁₁H₁₇ and Si₂₂H₂₁ clusters. The effect of the basis set superposition error (BSSE) was taken into account by applying the counterpoise correction. The calculated results indicated that the binding energies between hydrated Au⁺ cations and clean Si(1 1 1) surface are large, suggesting a strong interaction between hydrated Au⁺ cations and the semiconductor surface. The bonding nature of the chemical adsorption of Au⁺ to Si surface can be classified as partial covalent as well as ionic bonding. As the number of water molecules increases, the water molecules form hydrogen bond network with one another and only one water molecule binds directly to the Au⁺ cation. The Au⁺ cation in aqueous solution will safely attach to the clean Si(1 1 1) surface.     

Synchrotron radiation photoemission studies of the pentacene—Ag/Si(1 1 1) √3 × √3 interface

The interaction of monolayer coverages of pentacene with the √3 × √3 silver terminated Si(1 1 1) surface has been studies by high resolution core level and valence band photoemission spectroscopies. Core level Si 2p spectra reveal that there is only a very weak interaction between the pentacene and the underlying silicon, however, there is evidence of Fermi level movement. Valence band spectra acquired with both s and p polarised light indicate that for the surface coverages investigated, the molecular layers are oriented parallel to the plane of the surface. These results are in agreement with recent scanning tunneling microscopy (STM) studies which indicated that the pentacene molecules form highly ordered layers with the plane of the molecule parallel to the surface. Changes in the workfunction and Fermi level movements have been used to determine the energy level alignment at the interface. A 0.35 eV interface dipole forms between the pentacene and the silver terminated Si(1 1 1) surface within a two monolayer deposition. Photoemission measurements of the energy level alignment at the interface reveal that there is almost no barrier to charge injection from the conduction band of the semiconductor to the lowest unoccupied molecular orbital (LUMO) of the pentacene molecule.     

Theoretical investigation of Mn adsorbates aside self-organised Bi nanolines on hydrogenated Si(0 0 1) surface

We have theoretically investigated the atomic structure, magnetic behaviour, and electronic properties of Mn adsorbates on hydrogen passivated self-organised Bi nanolines on the Si(0 0 1)surface. It is found that the most stable geometry for monolayer (ML) coverage of Mn is just underneath the first Si(0 0 1) surface layer. The Mn atoms in the optimised configuration are seven-fold coordinated with their neighbouring Si atoms. Total energy calculations suggest that the Mn adsorbates form a degenerate state of ferromagnetic and anti-ferromagnetic lines parallel and adjacent to the self-assembled Bi lines. The density functional band structure calculation within the local-spin density approximation shows that the ferromagnetic system behaves like a metal in both spin channels. On the other side, the anti-ferromagnetic phase exhibits a half-metallic phenomenon with semiconducting character for the majority spin channel and semi-metallic character for the minority spin channel.     

Templated growth of quasi-one dimensional molecular structures on Si(1 1 1)-(4 × 1)-In surface

Self-assembly of quasi-one dimensional pentacene molecular chains are realized on Si(1 1 1) surface using the atomic chain structures of the well-defined Si(1 1 1)-(4 × 1)-In surface reconstruction as templates. It is determined that the molecules are adsorbed between two neighboring In chains with their long axis perpendicular to the chain direction. The molecular chains are grown with periodicity commensurate with the lattice constant in the In atomic chains. Our positive results suggest that this approach might be applied to grow organic hetero-nanostructures on specifically decorated semiconductor surfaces.     

Coverage dependent organic–metal interaction studied by high-resolution core level spectroscopy: SnPc (sub)monolayers on Ag(1 1 1)

We study the electronic structure of tin-phthalocyanine (SnPc) molecules adsorbed on a Ag(1 1 1) surface by high-resolution photoelectron spectroscopy. We particularly address the effect of different SnPc coverages on the interaction and charge transfer at the interface. The results give evidence for a covalent molecule–substrate interaction, which is temperature and coverage dependent. The valence and core level spectra as well as the work function measurements allow us monitoring subtle differences in the strength of the interface interaction, thus demonstrating the sensitivity of the methods. The results consistently show the effect of charge exchange between substrate and molecules which obviously leads to a net charge transfer into the SnPc molecules, and which is increased with decreasing coverage. Surprisingly, the Sn3d core levels are neither effected by variations of charge transfer and interaction strength, nor by a possible “Sn-up” or “Sn-down” orientation, which have been observed for sub-monolayers.     

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.     

Adsorption of an organic zwitterion on a Si(1 1 1)-7 × 7 surface at room temperature

The couple sulfonato/Si(1 1 1)-7 × 7 leads to remarkable 2D chiral molecular assembly with a stability improved at room temperature. The voltage-dependency of the STM images has been experimentally investigated and the correlation between STM images and PDOS has been studied. The proposed empirical model of the adsorption of molecules on Si(1 1 1)-7 × 7 has been justified by the experimental and theoretical data.     

Simulations of germanium epitaxial growth on the silicon (1 0 0) surface incorporating intermixing

We present kinetic lattice Monte Carlo simulations of Ge deposition onto a reconstructed Si (1 0 0) surface. We account for the exchange of Ge with Si atoms in the substrate, considering two different exchange mechanisms: a dimer exchange mechanism whereby Ge–Ge dimers on the surface become intermixed with substrate Si atoms, and the exchange of Ge atoms below the surface to relieve misfit strain. We examine how Si–Ge exchange affects the interface between the materials when the growth simulations are done at different temperatures.     

Growth mode and novel structure of ultra-thin KCl layers on the Si(1 0 0)-2 × 1 surface

This study investigates ultra-thin potassium chloride (KCl) films on the Si(1 0 0)-2 × 1 surfaces at near room temperature. The atomic structure and growth mode of this ionic solid film on the covalent bonded semiconductor surface is examined by synchrotron radiation core level photoemission, scanning tunneling microscopy and ab initio calculations. The Si 2p, K 3p and Cl 2p core level spectra together indicate that adsorbed KCl molecules at submonolayer coverage partially dissociate and that KCl overlayers above one monolayer (ML) have similar features in the valance band density of states as those of the bulk KCl crystal. STM results reveal a novel c(4 × 4) structure at 1 ML coverage. Ab initio calculations show that a model that comprises a periodic pyramidal geometry is consistent with experimental results.     

Structural properties of Cu clusters on Si(1 1 1):Cu2Si magic family

Basing on the results of the scanning tunneling microscopy (STM) observations and density functional theory (DFT) calculations, the structural model for the Cu magic clusters formed on Si(1 1 1)7 × 7 surface has been proposed. Using STM, composition of the Cu magic clusters has been evaluated from the quantitative analysis of the Cu and Si mass transport occurring during magic cluster converting into the Si(1 1 1)‘5.5 × 5.5’-Cu reconstruction upon annealing. Evaluation yields that Cu magic cluster accommodates 20 Cu atoms with 20 Si atoms being expelled from the corresponding 7 × 7 half unit cell (HUC). In order to fit these values, it has been suggested that the Cu magic clusters resemble fragments of the Cu₂Si-silicide monolayer incorporated into the rest-atom layer of the Si(1 1 1)7 × 7 HUCs. Using DFT calculations, stability of the nineteen models has been tested of which five models appeared to have formation energies lower than that of the original Si(1 1 1)7 × 7 surface. The three of five models having the lowest formation energies have been concluded to be the most plausible ones. They resemble well the evaluated composition and their counterparts are found in the experimental STM images.     

Initial stage of CdTe on Si(1 0 0) grown by MBE

The initial stage of CdTe growth on silicon has been investigated using angle-resolved photoemission and scanning tunneling microscopy (STM). In order to study initial stage of CdTe on Si, we have desorbed CdTe by annealing at 600 °C so that only one monolayer of Te remains on the Si(1 0 0) substrate. Te/Si(1 0 0)2×1 superstructure has been observed by LEED. Photoemission spectra indicate that Te atoms bond with the Si dangling bond. Atomically resolved STM images reveal that the Te atoms form dimers. It is observed that buckling direction of Te-dimer changes and the dimmers are broken in the site of some dimmer rows. It can be explained that the large lattice mismatch cause the switching of the buckling direction and the breaking of Te-dimer resulted surface relaxation.     

Tetra-σ bonding adsorption of pyridine on Si(1 0 0)-2 × 1

We studied adsorption of pyridine on Si(1 0 0) at room temperature using high resolution photoemission spectroscopy (PES) and near edge X-ray adsorption fine structure (NEXAFS) in the partial electron yield (PEY) mode. The Si 2p, C 1s, N 1s spectra of pyridine on Si(1 0 0) showed that pyridine is chemisorbed on Si(1 0 0)-2 × 1 through the formation of the tetra-σ-bonded structure with the N atom and three C atoms. NEXAFS was conducted to characterize the adsorption geometry of pyridine on Si(1 0 0). The π* orbital of CC bond showed a good angle dependence in C K-edge NEXAFS spectra, and we were able to estimate the adsorption angle between chemisorbed pyridine of CC bond and the Si(1 0 0) surface using an analytical solution of NEXAFS intensity. We find the coexistence of two different tight bridges with the adsorption angles 42 ± 2° and 45 ± 2° with almost equal abundance.     

Formation of a √3 × √3 surface on Si/Ge(1 1 1) studied by STM and LEED

We have performed a detailed study of the formation and the atomic structure of a √3 × √3 surface on Si/Ge(1 1 1) using both scanning tunneling microscopy (STM) and low energy electron diffraction (LEED). Both experimental methods confirm the presence of a √3 × √3 periodicity but unlike the Sn/Ge(1 1 1) and the Sn/Si(1 1 1) surfaces, the Si/Ge(1 1 1) surface is not well ordered. There is no long range order on the surface and the √3 × √3 reconstruction is made up of double rows of silicon atoms separated by disordered areas composed of germanium atoms.     

Configuration of pentacene (C22H14) films on Si(1 0 0)-2 × 1 studied by NEXAFS

Pentacene films on Si(1 0 0)-(2 × 1) surface at 300 K were investigated using near edge X-ray absorption fine structure (NEXAFS) at the carbon K-edge. NEXAFS spectra show that pentacene molecules are chemisorbed on the Si(1 0 0)-(2 × 1) surface for monolayer with flat-laying and predominantly physisorbed on the Si(1 0 0)-(2 × 1) surface for multilayer films with an upright molecular orientation. Absorption angle of pentacene molecules were measured through π^∗ transition. The angles between the double bond and the silicon surface were 35-55°, 65° and 76° at monolayer, 24 and 48 nm pentacene deposited on the Si(1 0 0) surface, respectively. We observed that the intermediate flat-laying phase is favored for monolayer coverage, while the films of molecules standing perpendicular to the Si(1 0 0) surface are favored for multilayer coverage.     

Molecular adsorption and growth of n-butane adlayers on Pt(1 1 1)

The molecular adsorption of n-butane and the growth of n-butane adlayers on Pt(1 1 1) was investigated using molecular beam techniques, temperature-programmed desorption (TPD) and low-energy electron diffraction (LEED). It is found that as the surface coverage of n-butane increases, structural changes occur in the adlayer at surface temperatures near 98 K that are accompanied by changes in the binding energy and mobility of the adsorbed species. The film growth process can be divided into four distinct coverage regimes. At low coverages (θ<0.14 ML, where 1 ML is defined as one butane molecule per Pt atom) a disordered monolayer forms in which the butane molecules prefer to lie parallel to the surface in order to minimize their binding energy. At coverages from 0.14 to 0.20 ML, ordered regions develop within the monolayer in which the butane molecules also lie parallel to the surface. The binding energy in the ordered phase is lower than that in the disordered phase due to repulsive intermolecular interactions. A more densely-packed ordered phase begins to form at 98 K after the low-coverage ordered phase saturates at 0.20 ML. The experimental results suggest that the n-butane molecules tilt away from the surface in the high-coverage ordered phase. Finally, a disordered second layer phase forms after the high coverage ordered phase saturates at 0.35 ML. The molecules in the second layer are very mobile at 98 K and rapidly diffuse to the edges of the beam spot. Interchange of molecules between the second layer and ordered monolayer is found to govern the net rate of second layer diffusion at surface temperatures less than 133 K. The adsorption probability of n-butane on Pt(1 1 1) continuously increases with increasing coverage, with no significant dependencies on the structure of the n-butane adlayer. This finding indicates that the long-range arrangements and molecular orientations of a mobile alkane adlayer have a negligible influence on the intrinsic adsorption dynamics, suggesting that the energy transfer processes that facilitate adsorption are highly localized.     

The origin of inter-dimer-row correlated adsorption for NH3 on Si(0 0 1)

We discuss the interaction between adsorbing ammonia molecules and pre-adsorbed ammonia fragments on the Si(0 0 1) surface, searching for experimental evidence of a H-bonded precursor state predicted by modelling. While correlations along dimer rows have already been identified, these mix substrate-mediated effects due to dimer buckling with ammonia–adsorbate effects. Correlations between fragments on neighbouring dimer rows are not affected by substrate effects (in this system), allowing an analysis of direct ammonia–adsorbate effects. We present an analysis of cross-row correlations in existing high-coverage STM data which shows significant correlations between NH₂ groups on neighbouring dimer rows over a significant range, providing evidence for the H-bonded precursor state with a range of around 10 Å. We discuss implications for the interpretation of STM images of ammonia on Si(0 0 1).     

Magnetization reorientation in Ni (1 1 1) ultrathin films studied by low-temperature hysteresis measurements

Surface magneto-optical Kerr effect (SMOKE) magnetometry in the temperature range 10–300 K was exploited to investigate the magnetic properties of high-quality Cu/Ni/Cu/Si(1 1 1) epitaxial heterostructures with thickness of the Ni layer, d_Ni, between 10 and 60 Å. For a fixed temperature, the equilibrium direction of the magnetization is parallel or perpendicular to the film surface, depending on the Ni thickness, because of the competition among shape anisotropy, magnetoelastic anisotropy and interface anisotropy. No reorientation of the magnetization could be observed as a function of temperature, for any of the specimens analyzed, while a large variation of the loop squareness and coercivity was found. This last variation has been qualitatively explained using a theoretical model based on a Green's function technique, valid for a monodomain film with a coherent rotation of the magnetization.