H3 Sites Research Articles

The [formula omitted] reconstruction on hexagonal 6H–SiC([formula omitted]) surface with and without a Si flux

The (3×3)R30° reconstruction on hexagonal 6H–SiC(0001) surface and its properties were studied by using reflection high-energy electron diffraction (RHEED) and RHEED multislice dynamical calculations. A Si coverage of 1/3 monolayer occupying the threefold-symmetric T4 or H3 sites develops upon a lower Si flux and/or at a higher annealing temperature and/or upon a longer time annealing. However, Si trimers centered on the T4 positions with 1 monolayer coverage may be another appropriate candidate for the (3×3)R30° reconstruction obtained under a very Si-rich condition and/or at a lower annealing temperature and/or upon a shorter time annealing.

Highly Specific Antibodies Determine Histone Acetylation Site Usage in Yeast Heterochromatin and Euchromatin

We have developed a highly specific antibody set for acetylation sites in yeast histones H4 (K5, K8, K12, and K16); H3 (K9, K14, K18, K23, and K27); H2A (K7); and H2B (K11 and K16). Since ELISA does not assure antibody specificity in chromatin immunoprecipitation, we have employed additional screens against the respective histone mutations. We now show that telomeric and silent mating locus heterochromatin is hypoacetylated at all histone sites. At the INO1 promoter, RPD3 is required for strongly deacetylating all sites except H4 K16, ESA1 for acetylating H2A, H2B, and H4 sites except H4 K16, and GCN5 for acetylating H2B and H3 sites except H3 K14. These data uncover the in vivo usage of acetylation sites in heterochromatin and euchromatin.

Carbon-induced reconstructions on Si(111) investigated by RHEED and molecular dynamics

The adsorption of carbon trimers on Si(1 1 1) 1×1 is investigated by means of empirical molecular dynamics based on a Tersoff potential. A priori unknown carbon terminated Si(1 1 1) surfaces are modeled. The energetics of different adsorption sites, specifically the S5, T4 and H3 sites are investigated. The obtained structural models are used to simulate their response to a RHEED experiment. This enables us to further elucidate on the feasibility of the models by comparing theoretical data to in situ RHEED observations during the MBE experiments. Implications of the models to growth of 3C SiC by carbonization are discussed.

Atomic models of (√3×√3)R30° reconstruction on hexagonal 6H–SiC(0001) surface

By using reflection high-energy electron diffraction (RHEED) and RHEED multislice dynamical calculations, the atomic structures of the (∛×∛)R30° reconstruction on 6H–SiC(0001) surface were solved. Both the simple adatom structure with a Si coverage of one-third monolayer occupying the threefold-symmetric T4 or H3 sites and a bit complex structure with Si trimers centered on the T4 positions with 1 monolayer coverage are all compatible with our results.

Origin, symmetry, and temperature dependence of the perturbation induced by Si extrinsic defects on the Sn/Si(111) α surface: A scanning tunneling microscopy study

We have studied with variable temperature scanning tunneling microscopy (STM) experiments the local structure of substitutional Si defects of the 1/3 ML Sn/Si(111) α surface. Empty state images show that most substitutional Si defects drift toward H3 sites leaving an unsaturated dangling bond from the first layer Si atoms. Consequently there is a charge transfer toward the Sn first neighbors of the defect. Filled state images show defect centered perturbations having 3×3 symmetry, which locally modifies the surface into a honeycomb pattern. Low temperature (120 K) STM images show undoubtedly the increase of the decay length of such perturbation, indicating the possibility of an overall phase transition at much lower temperatures.

Yeast HOS3 forms a novel trichostatin A-insensitive homodimer with intrinsic histone deacetylase activity.

Histone deacetylases such as human HDAC1 and yeast RPD3 are trichostatin A (TSA)-sensitive enzymes that are members of large, multiprotein complexes. These contain specialized subunits that help target the catalytic protein to histones at the appropriate DNA regulatory element, where the enzyme represses transcription. To date, no deacetylase catalytic subunits have been shown to have intrinsic activity, suggesting that noncatalytic subunits of the deacetylase complex are required for their enzymatic function. In this paper we describe a novel yeast histone deacetylase HOS3 that is relatively insensitive to the histone deacetylase inhibitor TSA, forms a homodimer when expressed ectopically both in yeast and Escherichia coli, and has intrinsic activity when produced in the bacterium. Most HOS3 protein can be found associated with a larger complex in partially purified yeast nuclear extracts, arguing that the HOS3 homodimer may be dissociated from a very large nuclear structure during purification. We also demonstrate, using a combination of mass spectrometry, tandem mass spectrometry, and proteolytic digestion, that recombinant HOS3 has a distinct specificity in vitro for histone H4 sites K5 and K8, H3 sites K14 and K23, H2A site K7, and H2B site K11. We propose that while factors that interact with HOS3 may sequester the catalytic subunit at specific cellular sites, they are not required for HOS3 histone deacetylase activity.

Use of ultrathin ZnSe dipole layers for band offset engineering at Ge and Si homo/heterojunctions

The ability to control semiconductor band discontinuities would allow solid devices to be specifically tailored so that efficiency and performance could be dramatically improved. This article reports the use of an ordered ZnSe monolayer to induce a valence band discontinuity at the Ge homojunction (0.38 eV), at the Ge–Si heterojunction (0.53 eV), and at the Si homojunction (∼0.2 eV). Soft x-ray photoemission was used to probe the interfaces as they were formed under ultrahigh vacuum conditions. The effect of overlayer band bending on the interpretation of band offset measurements is discussed. As the interfacial bonding and orientation of the dipole layer are key factors in determining the direction and magnitude of the band modification, x-ray standing wave measurements were performed on the Ge–ZnSe–Ge systems to identify the atomic structure of the junction. Se atoms were always found to bond to the Ge substrate in the a-top position, while the Zn atoms adopted the H3 sites, bonding to the overlayer. The results for these interfaces are interpreted in terms of the charge transfer; other factors such as strain and order are also addressed.

Migration process of an Al adatom on the Si(111) surface

Ab-initio quantum chemical calculations by density functional theory have been performed to investigate the migration process of an Al adatom on the Si(111) surface. The most stable adsorption site of a single Al adatom has been confirmed to be the T4 site, and the Al adsorption on the H3 site is also demonstrated to be a stable structure. In order to determine the probable Al migration path on the 1×1 area of the Si(111) surface, the potential energy changes during the movement of an Al adatom have been calculated. Computational results have clarified that the shortest path connecting the T4 site with the H3 site is the lowest potential energy route for Al diffusion. The activation energy barrier along this path has been estimated to be 0.9eV.

GaN(0001) surface structures studied using scanning tunneling microscopy and first-principles total energy calculations

Surface reconstructions occurring on the (0001) surface of wurtzite GaN are studied using scanning tunneling microscopy, electron diffraction, and Auger electron spectroscopy. The family of reconstructions found on this face includes 2×2, 5×5, 6×4, and ‘1×1’, in order of increasing surface Ga/N ratio. Detailed experimental results are presented for each of these reconstructions. First-principles total energy calculations are employed to identify possible model structures. An adatom model, with N-adatoms occupying H3 sites, is proposed for the 2×2 reconstruction. A model composed of N adatoms, Ga adatoms, and Ga vacancies is proposed for the 5×5 reconstruction.

Structural Investigation of the First Stages of Pyrolysis of Si-C-O Preceramic Polymers Containing Si–H Bonds

The polymer-to-glass transformation in the Si-C-O system usually involves cross-linking reactions at the C sites, which transform for example ≡Si–\(\underline {\text{C}} \)H3 sites into \(\underline {\text{C}} \)(Si)4 sites, leading to the formation of a silicon oxycarbide network. Identification of the various C sites that form during pyrolysis under inert atmosphere is rather difficult from 13C MAS-NMR spectra, due to strong overlap of resonance lines, which prevents an accurate determination of the chemical shift values. This paper reports on the use of a spectral editing technique called Inversion Recovery Cross Polarization (IRCP), which, when combined with Cross Polarization (CP) technique, allows us to identify and quantify the formation of Si-\(\underline {\text{C}} \)H2-Si bridges during the early stages of the pyrolytic transformation of a polysiloxane containing Si–CH3 and Si–H groups. Several Si-C-O systems characterized by the same initial number of Si–CH3 bonds but with increasing number of Si–H bonds, have been investigated by MAS-NMR as well as thermogravimetric analysis coupled with mass spectrometry (TG/MS). The Si—H bonds play clearly an active role in the insertion of C atoms within the silica network.

Essential and redundant functions of histone acetylation revealed by mutation of target lysines and loss of the Gcn5p acetyltransferase.

The Gcn5p histone acetyltransferase exhibits a limited substrate specificity in vitro. However, neither the specificity of this enzyme in vivo nor the importance of particular acetylated residues to transcription or cell growth are well defined. To probe these questions, we mutated specific lysines in the N-termini of histones H3 and H4 and examined the effects of these mutations in yeast strains with and without functional GCN5. We found that in vivo, GCN5 is required either directly or indirectly for the acetylation of several sites in H3 and H4 in addition to those recognized by the recombinant enzyme in vitro. Moreover, in the absence of GCN5, cells accumulate in G2/M indicating that Gcn5p functions are important for normal cell-cycle progression. Mutation of K14 in H3, which serves as the major target of recombinant Gcn5p acetylation in vitro, confers a strong, synthetic growth defect in gcn5 cells. Synergistic growth defects were also observed in gcn5 cells carrying mutations in lysine pairs (K8/K16 or K5/K12) in histone H4. Strikingly, simultaneous mutation of K14 in H3 and K8 and K16 in H4 to arginine, or deletion of either the H3 or the H4 N-terminal tail, results in the death of gcn5 cells. Mutation of these same three sites to glutamine is not lethal. Indeed, this combination of mutations largely bypasses the need for GCN5 for transcriptional activation by Gal4-VP16, supporting an important role for histone acetylation in Gcn5p-mediated regulation of transcription. Our data indicate that acetylation of particular lysines in histones H3 and H4 serves both unique and overlapping functions important for normal cell growth, and that a critical overall level of histone acetylation is essential for cell viability.

First principles calculations of the different structures of a monolayer of Sb on Si (111)

We have performed first-principles calculations to determine the surface atomic structure of a monolayer of Sb on the Si (111) surface. Scanning tunneling microscopy and low energy electron diffraction experiments have found (1×1), (2×1), and (∛×∛) reconstructions. Our calculations show that several structures have similar total energies, suggesting that different Sb geometries can coexist on Si (111). Besides the structures previously observed experimentally, we found a new structure (with similar total energy) formed by a sequence of two kind of trimers: one centered on a T4 site and the following on a H3 site.

Theory of interfaces and surfaces in wide-gap nitrides

A selection of the results of a theoretical investigation of the properties of interfaces and surfaces of the wide-gap III–V nitride semiconductors is reviewed. The electronic properties of wurtzite heteroepitaxial interfaces of AlN and GaN, incorporating the effects of strain, are discussed. In particular, we find that this interface is of type I and have calculated the valence-band offset to be −0.57 eV. The surface energies and atomic geometries of the 2×2 reconstructions of the (0001) face of GaN are also presented. In conditions which are rich in a given species, an adatom reconstruction of that species is found to be the most energetically favorable: for gallium-rich conditions, the reconstruction with a gallium adatom on a T3 site is the most stable, while for nitrogen-rich conditions the reconstruction with a nitrogen adatom on the H3 site is energetically the most favorable.

Surface atomic structure of epitaxially grown erbium silicide films on Si(111)7×7

The surface atomic structure of erbium silicide films epitaxially grown on Si(111)7\ifmmode\times\else\texttimes\fi{}7 by deposition in situ has been investigated by scanning tunneling microscopy (STM) and synchrotron radiation core-level photoelectron spectroscopy. For a film thickness of less than 1 ML, a silicide with a p(1\ifmmode\times\else\texttimes\fi{}1) low-energy electron-diffraction pattern is formed. Atomic resolution images reveal that this structure consists of a buckled Si double layer with atomic positions of the surface atoms very close to the ideal 1\ifmmode\times\else\texttimes\fi{}1 Si(111) surface. Thicker silicide films exhibit a ($\sqrt{3}$\ifmmode\times\else\texttimes\fi{}$\sqrt{3}$)R(30\ifmmode^\circ\else\textdegree\fi{}) superstructure usually attributed to an ordered network of Si vacancies. Atomic resolution STM images show that the surface termination for the bulk silicide also consists of a double-height Si layer where the superstructure is due to a small displacement of the upper Si atoms toward either T4 or H3 sites. As shown by core-level photoemission spectroscopy of the Si 2p peak as a function of the emission angle, the silicide does not show significant charge transfer within the surface layer. STM images directly exclude the presence of vacancies on the topmost Si layer.

Comparison of the first stages of the adsorption of Cs and Ge on the Si(111)7 × 7 surface

Experimental results show that Cs adsorbs preferentially on the threefold hollow (H3) and threefold filled (T4 sites of the Si(111)7 × 7 reconstructed surface. Following our recent calculations, adsorption of Ge on H3 or T4 sites of Si(111)7 × 7 is unfavourable. We present a comparative study of various adsoption mechanisms for Ge and Cs on Si(111)7 × 7, in the framework of the crystalline extension of the extended Hückel theory. We consider the possibility of Cs and Ge adsorption on T4 and H3 sites, corner and center adatoms, as well as restatoms. The faulted and unfaulted parts of the 7 × 7 unit cell are distinguished. Adsorption energies and reduced overlap population calculations effectively favour adsorption on the Si dangling bonds for Ge atoms and addition on H3 and T4 sites for Cs atoms. The cesium atom has diffuse orbitals, so that, at these positions, it can significantly interact with the dangling bonds despite the long distance. We discuss the differences of the behaviour between germanium and cesium interacting with Si(111)7 × 7.

Novel histamine H3 receptor antagonists: affinities in an H3 receptor binding assay and potencies in two functional H3 receptor models

1. We determined the affinities of ten novel H3 receptor antagonists in an H3 receptor binding assay and their potencies in two functional H3 receptor models. The novel compounds differ from histamine in that the aminoethyl side chain is replaced by a propyl or butyl chain linked to a polar group (amide, thioamide, ester, guanidine, guanidine ester or urea) which, in turn, is connected to a hexocyclic ring or to an alicyclic ring-containing alkyl residue [corrected]. 2. The specific binding of [3H]-N alpha-methylhistamine to rat brain cortex membranes was monophasically displaced by each of the ten compounds at pKi values ranging from 7.56 to 8.68. 3. Inhibition by histamine of the electrically evoked tritium overflow from mouse brain cortex slices preincubated with [3H]-noradrenaline was antagonized by the ten compounds and the concentration-response curve was shifted to the right with apparent pA2 values ranging from 7.07 to 9.20. 4. The electrically induced contraction in guinea-pig ileum strips (which was abolished by atropine) was inhibited by the H3 receptor agonists R-(-)-alpha-methylhistamine (pEC50 7.76), N alpha-methylhistamine (7.90) and imetit (8.18). The concentration-response curve of R-(-)-alpha-methylhistamine was shifted to the right by thioperamide (apparent pA2 8.79) and by the ten novel compounds (range of pA2 values 6.64-8.81). 5. The affinities and potencies were compared by linear regression analysis. This analysis was extended to thioperamide, the standard H3 receptor antagonist, which is also capable of differentiating between H3A and H3B sites. Comparison of the apparent pA2 values in the two functional H3 receptor models yielded a regression coefficient of 0.77 (P<0.02). When the pA2 of the drugs in the mouse brain cortex were compared to the pXj for H3 sites (ten novel compounds) and for H3A sites (thioperamide), a significant correlation (r = 0.87; P<0.001) was obtained. There was, however, no significant correlation when the pKi of thioperamide for H3B sites was used instead (r = 0.52). In a similar manner, comparison of the pA2 in the guinea-pig ileum with the pKi in the binding assay yielded a significant correlation(r = 0.70, P <0.05) only when the pKi of thioperamide for H3A sites was used but not when its pKi forH3B sites was considered (r = 0.17, NS).6 On the basis of these results, structure-activity relationships for the novel H3 receptor antagonists,and the nature of the H3 receptors in the guinea-pig ileum and mouse brain, are considered.

Adsorption of hydrogen atoms on the silicon(111) (1*1) surface: first-principles calculations

With a first-principles method, the energy surface of hydrogen atoms diffusing on the silicon(111) (1*1) surface and the energy curves of H atoms approaching the Si(111) (1*1) surface from three high-symmetry sites were calculated. The three high-symmetry sites (denoted as the T1, T4 and H3 sites) correspond to positions on top of the first (T1), second (T4) and fourth (H3) layers of the Si atoms. It was found that two of the high-symmetry sites (T4 and H3) correspond to local maxima on the adsorption energy surface while the third one (T1) is the chemisorbed site, i.e. that with the lowest adsorption energy. The completely different characteristics for the three sites of the same symmetry are related to how much the charges transfer from the surface dangling bonds to the H atoms in the adatom structures. It was also found that no local minimum exists on the energy surface and that there is a saddle point. When the coverage varies from one monolayer to 1/2 or 1/4 monolayer, the changes in the adsorption energies for H atoms adsorbed at the three high-symmetry sites are, at most, around 0.2 eV/H. Finally, the energy curves for H atoms approaching the Si surface through the T1 and T4 sites exhibit the familiar strong repulsion near the surface. However the energy curve is soft through the H3 sites even when there is already one monolayer coverage of H atoms at the T1 sites of the surface. The energy barrier for H atoms to penetrate into the bulk through the H3 sites is not larger than 0.3 eV. The large negative formation energies for H atoms residing at several locations beneath the surface demonstrate that penetration of the H atoms into the bulk can easily occur.

Structure of Ge(111) sqrt 3 x sqrt 3 R30 degrees-Au determined by surface x-ray diffraction.

The structure of the Ge(111)\ensuremath{\surd}3 \ifmmode\times\else\texttimes\fi{} \ensuremath{\surd}3 R30\ifmmode^\circ\else\textdegree\fi{}-Au reconstruction has been measured with surface x-ray diffraction. In-plane and out-of-plane scattering show that the basic structural unit is a trimer of Au atoms embedded in a single layer of Ge with small relaxations of the underlying substrate down to the second complete bilayer. The Au-Au intermetallic distance is 2.81 \AA{}, which is close to the bulk value of Au. The model is similar to the \ensuremath{\surd}3 \ifmmode\times\else\texttimes\fi{} \ensuremath{\surd}3 R30\ifmmode^\circ\else\textdegree\fi{} reconstructions formed by Au on Si(111) and Ag on Ge(111). These are characterized by an inward relaxation of the metal atoms from the threefold-hollow H3 sites towards the fourfold T4 site, in contrast to the reconstruction formed by Ag on Si(111), which exhibits an outward relaxation. The difference in behavior can be understood in terms of the relative bond energies.

Multisite occupancy at the alkali/silicon (111) interface studied with XSW

In this paper the authors report the results of an X-ray standing wave (XSW) study of an Si(111) 7*7-alkali metal (Cs,Rb) interface as a function of coverage. The three-fold hollow (H3) site, the three-fold filled (T4) site and all the dangling bond sites (atop, adatoms and vacancy) have been considered as available sites at the Si surface for the adsorbate. Although measurements have been recorded only for the (111) and the (111) diffracting planes and the number of sites is quite high, well defined distributions of the occupancy probabilities in the different sites fi for each sample, can be found assuming the adsorbate-substrate bond length and the substrate atomic coordinates of the reconstructed surface. The authors' results indicate a relaxation of the substrate atoms under the H3 and T4 sites.

Scanning Tunneling Microscopy for Hydrogen-Desorptioninduced Structural Change of Si(111) Surface

AbstractA scanning tunneling microscopy (STM) has revealed an atomic structure of Si(111)-√3× √3R30° which is induced by the hydrogen desorption at about 500 °C. There exist domains with the √3× √3R30° structures, indicating that each domain is formed by rearrangement of Si adatoms around each cluster present at room temperature. Near the domain boundary, the adatoms locate mostly at T4 sites and occasionally at H3 sites. The dynamic nature of the adatoms are predicted.