Low-coverage Phase Research Articles

Alternative characterization of the nematic transition in deposition of rods on two-dimensional lattices.

We revisit the problem of excluded volume deposition of rigid rods of length k unit cells over square lattices. Two new features are introduced: (a) two new short-distance complementary order parameters, called Π and Σ, are defined, calculated, and discussed to deal with the phases present as coverage increases; (b) the interpretation is now done beginning at the high-coverage ordered phase which allows us to interpret the low-coverage nematic phase as an ergodicity breakdown present only when k≥7. In addition the data analysis invokes both mutability (dynamical information theory method) and Shannon entropy (static distribution analysis) to further characterize the phases of the system. Moreover, mutability and Shannon entropy are compared, and we report the advantages and disadvantages they present for their use in this problem.

Lateral electronic screening in quasi-one-dimensional plasmons

The properties of one-dimensional (1D) plasmons are rather unexplored. We investigated the plasmonic collective excitations, measured as one-dimensional plasmon dispersions with electron energy loss spectroscopy, highly resolved both in energy and lateral momentum, for both phases of Au induced chains on stepped Si(553) substrates. We observe 1D dispersions that are strongly influenced by the lateral chain width and by the interchain coupling. Indications for the existence of two different plasmons originating from two surface bands of the systems are given for the low coverage phase.

Structure of Low and High Coverage Phases of Bromine on Pd(110)

Halogens can be used to steer the catalytic selectivity of transition metal surfaces. In the present work the structures of bromine on Pd(110) in the low-coverage c(2 × 4) and the high-coverage c(4 × 2) adlayers are investigated by density functional theory calculations and quantitative low-energy electron diffraction. Excellent agreement is achieved between theory and experiment. Both find the high-coordinated hollow site to be favored at low coverage, while in the high coverage phase also adsorption close to long-bridge sites occurs due to the Br–Br repulsion. This results in an almost uniform distribution of adatoms in the troughs of the Pd(110) surface as in the majority of halogen fcc(110) transition metal adsorption systems, but not on Pt(110). The different coordination of the hollow and quasi long-bridge adsorption sites is reflected by different distances to the top-layer Pd atoms, 271 pm for the high-coordinated hollow site and 248 pm for the low-coordinated quasi long-bridge site. With increasing bromine coverage the contraction of the first interlayer distance d12 of clean Pd(110) is reduced and inverted to an expansion of ∼3% at high bromine coverage. As shown by DFT, this change in substrate relaxation depends markedly on the adsorption site. A population analysis reveals a non-negligible ionic contribution for the Br–Pd bonding. Finally, we discuss the, at first sight, surprising DFT prediction of pure long-bridge adsorption at intermediate coverages.

Understanding the Phase Diagram of Self-Assembled Monolayers of Alkanethiolates on Gold.

Alkanethiolate monolayers on gold are important both for applications in nanoscience as well as fundamental studies of adsorption and self-assembly at metal surfaces. While considerable experimental effort has been put into understanding the phase diagram of these systems, theoretical work based on density functional theory (DFT) has long been hampered by the inability of conventional exchange-correlation functionals to describe dispersive interactions. In this work, we combine dispersion-corrected DFT calculations using the new vdW-DF-CX functional with the ab initio thermodynamics method to study the stability of dense standing-up and low-coverage lying-down phases on Au(111). We demonstrate that the lying-down phase has a thermodynamic region of stability starting from thiolates with alkyl chains consisting of n ≈ 3 methylene units. This phase emerges as a consequence of a competition between dispersive chain–chain and chain–substrate interactions, where the strength of the latter varies more strongly with n. A phase diagram is derived under ultrahigh-vacuum conditions, detailing the phase transition temperatures of the system as a function of the chain length. The present work illustrates that accurate ab initio modeling of dispersive interactions is both feasible and essential for describing self-assembled monolayers.

Interlocus gene conversion explains at least 2.7% of single nucleotide variants in human segmental duplications.

BackgroundInterlocus gene conversion (IGC) is a recombination-based mechanism that results in the unidirectional transfer of short stretches of sequence between paralogous loci. Although IGC is a well-established mechanism of human disease, the extent to which this mutagenic process has shaped overall patterns of segregating variation in multi-copy regions of the human genome remains unknown. One expected manifestation of IGC in population genomic data is the presence of one-to-one paralogous SNPs that segregate identical alleles.ResultsHere, I use SNP genotype calls from the low-coverage phase 3 release of the 1000 Genomes Project to identify 15,790 parallel, shared SNPs in duplicated regions of the human genome. My approach for identifying these sites accounts for the potential redundancy of short read mapping in multi-copy genomic regions, thereby effectively eliminating false positive SNP calls arising from paralogous sequence variation. I demonstrate that independent mutation events to identical nucleotides at paralogous sites are not a significant source of shared polymorphisms in the human genome, consistent with the interpretation that these sites are the outcome of historical IGC events. These putative signals of IGC are enriched in genomic contexts previously associated with non-allelic homologous recombination, including clear signals in gene families that form tandem intra-chromosomal clusters.ConclusionsTaken together, my analyses implicate IGC, not point mutation, as the mechanism generating at least 2.7 % of single nucleotide variants in duplicated regions of the human genome.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1681-3) contains supplementary material, which is available to authorized users.

Helium Diffraction Study of Low Coverage Phases of Mercaptoundecanol and Octadecanethiol Self-Assembled Monolayers on Au(111) Prepared by Supersonic Molecular Beam Deposition

Thiol self-assembled monolayers (SAMs) on Au(111) are ubiquitous systems for surface functionalization. While these systems have been studied extensively in the past there are still points that need further investigation both from a fundamental surface science point of view and an application point of view. For instance, SAMs of long chain thiols which are solid at room temperature have only been grown in solution due to their low vapor pressure. Hence, almost all the reported properties of these SAMs, such as growth mechanism, kinetics, and film structures, are based on solution-grown films. Here long chain thiol SAMs were grown in vacuum by using supersonic molecular beam (SMBD) deposition. This technique not only allows low vapor pressure thiols to be deposited in vacuum in a very controlled way, but it also enables control over the kinetic energies of the deposited molecules. Here we report a helium diffraction study of low coverage striped phases of mercaptoundecanol (MUD) and octadecanethiol (ODT) SAMs on the Au(111) surface. MUD SAMs were observed to form a (11.8 × √3) unit cell whereas ODT SAMs adopt a (18 × √3) unit cell. Both of the studied molecules were shown to form disordered physisorbed layers on the chemisorbed first layer, with desorption energies of 72 and 86 kJ/mol, respectively. While four desorption states could be identified for MUD with energies of 118, 136, 141, and 150 kJ/mol, ODT has one chemisorbed and one physisorbed state with desorption energies of 135 and 154 kJ/mol. The results reported here may serve as a reference for comparison of properties of solution-grown and vacuum-deposited thiol SAMs. In addition, the control over the kinetic energy may open up new possibilities in terms of applications that utilize patterned films.

Helium atom diffraction study of low coverage phases of decanethiol self-assembled monolayers prepared by supersonic molecular beam deposition

Thiol self-assembled monolayers (SAMs) on gold surfaces have a wide range of applications including surface patterning and metal contact–organic semiconductor interface modification in organic electronic devices. Here we present our studies about the low coverage phases of decanethiol (CH3(CH2)9SH) SAMs on Au(111) surface, grown in vacuum by supersonic molecular beam deposition. Crystal structures, phase behaviors and desorption energies of these films determined by helium atom diffraction technique are discussed.

Adsorption and thermal decomposition of 2-octylthieno[3,4-b]thiophene on Au(1 1 1)

The adsorption and thermal stability of 2-octylthieno[3,4-b]thiophene (OTTP) on the Au(111) surfaces have been studied using scanning tunneling microscopy (STM), temperature programmed desorption (TPD), and X-ray photoelectron spectroscopy (XPS). UHV-STM studies revealed that the vapor-deposited OTTP on Au(111) generated disordered adlayers with monolayer thickness even at saturation coverage. XPS and TPD studies indicated that OTTP molecules on Au(111) are stable up to 450K and further heating of the sample resulted in thermal decomposition to produce H2 and H2S via C–S bond scission in the thieno-thiophene rings. Dehydrogenation continues to occur above 600K and the molecules were ultimately transformed to carbon clusters at 900K. Highly resolved air-STM images showed that OTTP adlayers on Au(111) prepared from solution are composed of a well-ordered and low-coverage phase where the molecules lie flat on the surface, which can be assigned as a (9×2√33)R5° structure. Finally, based on analysis of STM, TPD, and XPS results, we propose a thermal decomposition mechanism of OTTP on Au(111) as a function of annealing temperature.

Deprotonated Glycine on Cu(111): Quantitative Structure Determination by Energy-Scanned Photoelectron Diffraction

The local adsorption site of the deprotonated simple amino acid glycine (glycinate) on Cu(111) has been investigated quantitatively by O 1s and N 1s energy-scanned photoelectron diffraction (PhD). The nitrogen atom is found to adsorb in a near-atop site with a Cu–N bond length of 2.02 ± 0.02 Å. However, based on the PhD data alone there is some ambiguity in the adsorption sites occupied by the oxygen atoms, although at least one of these atoms occupies a near-atop site with a Cu–O bond length of 2.00–2.02 ± 0.02–0.07 Å. Density functional theory (DFT) calculations have also been conducted on simple models (a low-coverage (3 × 3) phase of noninteracting molecules and a higher-coverage ordered (4 × 4) structure). The structural conclusions of the DFT calculations proved to be very sensitive to the use of different functionals and failed to resolve the structural ambiguity of the PhD analysis fully, but a single tridentate-bonding structural model appears to be most consistent with the PhD, DFT, and supporting spectroscopic information from previous studies.

Structure of CO2 Adsorbed on the KCl(100) Surface

The structure and dynamics of the adsorbate CO(2)/KCl(100) from a diluted phase to a saturated monolayer have been investigated with He atom scattering (HAS), low-energy electron diffraction (LEED), and polarization dependent infrared spectroscopy (PIRS). Two adsorbate phases with different CO(2) coverage have been found. The low-coverage phase is disordered at temperatures near 80 K and becomes at least partially ordered at lower temperatures, characterized by a (2√2×√2)R45° diffraction pattern. The saturated 2D phase has a high long-range order and exhibits (6√2×√2)R45° symmetry. Its isosteric heat of adsorption is 26 ± 4 kJ mol(-1). According to PIRS, the molecules are oriented nearly parallel to the surface, the average tilt angle in the saturated monolayer phase is 10° with respect to the surface plane. For both phases, structure models are proposed by means of potential calculations. For the saturated monolayer phase, a striped herringbone structure with 12 inequivalent molecules is deduced. The simulation of infrared spectra based on the proposed structures and the vibrational exciton approach gives reasonable agreement between experimental and simulated infrared spectra.

Scanning Tunneling Microscopy and Cyclic Voltammetry Study of Self-Assembled 3,3′-Thiobis(1-propanesulfonic acid, sodium salt) Monolayers on Au(111) Electrodes

Self-assembled monolayers (SAMs) of 3,3′-thiobis(1-propanesulfonic acid, sodium salt) (TBPS) on Au(111) electrodes have been characterized by scanning tunneling microscopy and cyclic voltammetry in aqueous perchloric acid solutions. TBPS exhibits an adsorption behavior typically observed for dialkyl sulfides including intact adsorption and low coverage phases with molecules predominantly lying flat on the surface. On the other hand, an untypical chemical bond and well-ordered domains were determined which resemble the characteristics of alkenethiol SAMs. When the adlayer was prepared at its open circuit potential (OCP), a (6 × 3√3) TBPS adlayer phase was observed at potentials E > 0.7 VRHE in TBPS-free electrolyte. At more cathodic potentials, the adlayer transforms irreversible to a disordered phase. In contrast, in situ STM studies in TBPS-containing electrolyte reveal a very complex, potential-dependent adsorption behavior. With increasing electrode potential, the structure of the adlayer transforms in...

Structural investigation of Au(111)/butylthiolate adsorption phases

The structures of the high-coverage ('standing-up') and low-coverage ('lying-down') phases of butylthiolate on Au(111) have been investigated by a range of experimental methods. Normal incidence X-ray standing waves, photoelectron diffraction and near-edge X-ray absorption fine structure results all identify the local S headgroup site as atop a surface Au atom in a bulk continuation site for both high- and low-coverage phases. Low energy electron diffraction shows the low-coverage phase to have a (12 x radical 3)rect. surface mesh with glide-line symmetry (pmg space group), the long dimension of this mesh being approximately four times the length of the butylthiolate molecule. A structural model is proposed for this phase based on two different enantiomers of an Au-adatom-dithiolate species that is consistent with these results and with recent finding for propylthiolate on this surface using low-temperature scanning tunnelling microscopy (O. Voznyy, J. J. Dubowski, J. T. Yates Jr. and P. Maksymovych, J. Am Chem. Soc., 2009, 131, 12989).

CO2 Adlayers on the Mixed Terminated ZnO(10-10) Surface Studied by He Atom Scattering, Photoelectron Spectroscopy and Ab Initio Electronic Structure Calculations

He-atom scattering (HAS), X-ray photoelectron spectroscopy (XPS and NEXAFS), periodic density functional theory and quantum chemical ab initio cluster calculations have been used for characterizing the adsorption of CO2 on the mixed terminated ZnO(10-10) surface. The HAS data allow to identify three different structural phases of CO2 in the monolayer regime: A high-density (1×1) phase at low temperature, a lower density (2×1) phase at higher temperatures, and in addition an incommensurate phase (which has not been reported before) with a slightly lower coverage and a 2.3-fold periodicity at surface temperatures above 270 K. XPS and NEXAFS measurements performed for the two low-coverage phases show that CO2 is adsorbed in form of a carbonate species. This is supported by the ab initio calculations for CO2 adsorbed on ZnO(10-10). The calculated XP and NEXAFS spectra agree with the experimental data and are only compatible with an adsorbed carbonate species, the presence of physisorbed CO2 can be excluded. In addition, the calculations demonstrate that X-ray emission spectroscopy (XES) is a sensitive method to distinguish between linear CO2 and carbonate.

Spontaneous Domain Switching during Phase Separation of Pb on Ge(111)

Using low-energy electron microscopy (LEEM), we have discovered a novel phase separation mechanism for Pb on Ge(111). When the low Pb coverage (1 x 1) phase coexists with the high coverage beta phase, the surface consists of approximately 100 nm sized domains that spontaneously switch from one phase to the other. We argue this striking mechanism occurs because nanometer-scale domains can have density fluctuations comparable to the density difference between the two phases.

Amino acid and peptides on Cu(1 1 0) surfaces: Chemical and structural analyses of l-lysine

Adsorption of l-lysine on a Cu(1 1 0) surface has been carried out under UHV condition from sublimation of a crystalline phase. The adsorption was characterised by FT-RAIRS, LEED and STM. At room temperature, the adsorption geometry of the lysine molecules varies as a function of the exposure. The low coverage phase sees the molecules adsorbed via the oxygen atoms of the deprotonated carboxylate group and the nitrogen atom of the amino group. Close to saturation monolayer regime, the molecules reorient to be anchored to the surface via one oxygen of a side way tilted carboxylate moiety and the interaction of the N atom of the amino group. When this high coverage phase is annealed up to 425 K, the chemical nature and the adsorption geometry stay similar. However, the study of each of these phases by LEED and STM has shown three different two-dimensional adlayers. At room temperature, the low coverage phase exhibits paired chains of molecules growing symmetrically at ±19° of the [0 0 1] direction, while the high coverage phase presents a chiral (−2, −2; 5, −1) chiral phase with an overall growth direction parallel to the [−1 1 2] direction. Finally, the high coverage phase warmed up to 425 K leads to a (3 × n) structure, which seems to be a stable intermediate overlayer at this temperature, that gives rise to a (3 × 2) structure when annealed to 450 K. A number of schematic adsorption geometry models are proposed for each phase.

Structural Investigation of the Interaction of Molecular Sulfur with Ag(111)

Scanning tunneling microscopy (STM) and normal-incidence X-ray standing wave (NIXSW) analysis, together with low-energy electron diffraction (LEED) and X-ray photoelectron spectroscopy (XPS), have been used to investigate the structure of surface phases formed by the dissociation of molecular sulfur (S2) on Ag(111) under ultrahigh vacuum conditions. Both a complex low coverage phase and the well-known Ag(111)(√7×√7)R19°-S surface have been investigated. In the case of the low coverage phase, the long-range periodicity seen in STM and the LEED pattern have been reconciled, while NIXSW data indicate a significant local coherence of the S atoms on the substrate. However, the complexity of this phase, with a minimum estimate of 11 S atoms per unit mesh, is too great for complete structural interpretation. A model for the (√7×√7)R19°-S phase, based on epitaxial growth of the high-temperature fcc phase of Ag2S(111), is found to be consistent with all the experimental data, while NIXSW provides information on th...

Langmuir Films of Anthracene Derivatives on Liquid Mercury II: Asymmetric Molecules

The structure and phase sequence of liquid-mercury-supported Langmuir films (LFs) of anthrone and anthralin were studied by surface tensiometry and surface-specific synchrotron X-ray diffraction. In the low-coverage phase the molecules are both side-lying, rather than the flat-lying orientation found for anthracene and anthraquinone. In the high-coverage phase, the molecules are either standing up (anthrone) or remain side-lying (anthralin) on the mercury surface. In contrast with the symmetric anthracene and anthraquinone, both high-coverage phases exhibit long-range in-plane order. The order is different for the two compounds. The structural details, the role of molecular symmetry, the oxygen side groups, and the asymmetry-induced dipole moments are discussed.

Interdiffusion of adsorbed Pb and Bi on Cu(1 0 0)

The impingement and interdiffusion of adsorbed Pb and Bi layers spreading from separated 3D pure bulk sources on Cu(1 0 0) has been studied, at T = 513 K, by in situ scanning Auger microscopy. When the leading edges of the pure Pb and Bi diffusion profiles impinge, they both consist of low-coverage lattice gas surface alloyed phases. In these low-coverage phases, Pb displaces surface alloyed Bi and the point of intersection of the profiles drifts towards the Bi source. These features lead to the conclusion that Pb atoms are more strongly bound at surface alloyed sites in Cu(1 0 0) than Bi atoms. Once the total coverage (Pb + Bi) on the substrate reaches about one monolayer, Pb and Bi are dealloyed from the substrate, and the interdiffusion profiles become essentially symmetric. Pb and Bi mix in all proportions, with an interdiffusion coefficient of ∼10 −13 m 2/s. This is considerably smaller than the self-diffusion coefficients previously observed for pure Pb and Bi in their respective high-coverage phases, indicating that the mechanism of interdiffusion is different from that of self-diffusion. As interdiffusion proceeds, the point of intersection of the Pb and Bi profiles reverses its drift direction, leading to the conclusion that binding of Bi atoms to the Cu(1 0 0) substrate is stronger than that of Pb atoms in the highest-coverage surface dealloyed layers.

Comparative study of Ag, Au, Pd, and Pt adsorption on Mo andTa(112)surfaces

The structural, energetic, and electronic properties of low-coverage phases of Ag, Au, Pd, and Pt atoms adsorbed on the (112) surface of Mo and Ta are investigated from first principles. On $\mathrm{Mo}(112)$ the binding energy of adatoms increases with coverage (for dimers, linear trimers, and infinite chains) which means the prevalence of attractive interactions between adatoms in the same trough and their clustering. This is at variance from the behavior on the Ta surface where the binding per adatom in dimers or trimers is decreasing or not altered compared to a single atom adsorption. Consequently, on $\mathrm{Mo}(112)$ adatom chains form in the furrows as experimentally observed, whereas on $\mathrm{Ta}(112)$ the adatoms are more likely to form a scattered, random pattern. Pd and Pt adsorbates are predicted to mix and alloy with $\mathrm{Ta}(112)$ atoms.

Response of a model of CO oxidation with CO desorption and diffusion to a periodic external CO pressure

We present a study of the dynamical behavior of a Ziff–Gulari–Barshad model with CO desorption and lateral diffusion. Depending on the values of the desorption and diffusion parameters, the system presents a discontinuous phase transition between low and high CO coverage phases. We calculate several points on the coexistence curve between these phases. Inclusion of the diffusion term produces a significant increase in the CO 2 production rate. We further applied a square-wave periodic pressure variation of the partial CO pressure with parameters that can be tuned to modify the catalytic activity. Contrary to the diffusion-free case, this driven system does not present a further enhancement of the catalytic activity, beyond the increase induced by the diffusion under constant CO pressure.