High Coverage Phase Research Articles

Entropy-driven phases at high coverage adsorption of straight rigid rods on two-dimensional square lattices.

Polymers are frequently deposited on different surfaces, which has attracted the attention of scientists from different viewpoints. In the present approach polymers are represented by rigid rods of length k (k-mers), and the substrate takes the form of an L×L square lattice whose lattice constant matches exactly the interspacing between consecutive elements of the k-mer chain. We briefly review the classical description of the nematic transition presented by this system for k≥7 observing that the high-coverage (θ) transition deserves a more careful analysis from the entropy point of view. We present a possible viewpoint for this analysis that justifies the phase transitions. Moreover, we perform Monte Carlo (MC) simulations in the grand canonical ensemble, supplemented by thermodynamic integration, to first calculate the configurational entropy of the adsorbed phase as a function of the coverage, and then to explore the different phases (and orientational transitions) that appear on the surface with increasing the density of adsorbed k-mers. In the limit of θ→1 (full coverage) the configurational entropy is obtained for values of k ranging between 2 and 10. MC data are discussed in comparison with recent analytical results [D. Dhar and R. Rajesh, Phys. Rev. E 103, 042130 (2021)2470-004510.1103/PhysRevE.103.042130]. The comparative study allows us to establish the applicability range of the theoretical predictions. Finally, the structure of the high-coverage phase is characterized in terms of the statistics of k×l domains (domains of l parallel k-mers adsorbed on the surface). A distribution of finite values of l (l≪L) is found with a predominance of k×1 (single k-mers) and k×k domains. The distribution is the same in each lattice direction, confirming that at high density the adsorbed phase goes to a state with mixed orientations and no orientational preference. An order parameter measuring the number of k×k domains in the adsorbed layer is introduced.

Understanding the interaction of organic corrosion inhibitors with copper at the molecular scale: Benzotriazole on Cu(110)

Benzotriazole (BTAH) has been used for several industrial applications, but most commonly as a corrosion inhibitor for copper, since the 1950s. However, the mechanism of its interaction with copper surfaces at the atomistic scale is still a matter of debate. Here, the adsorption of BTAH onto a clean Cu(110) surface has been investigated by a combination of scanning tunnelling microscopy, X-ray photoelectron spectroscopy, high resolution electron energy loss spectroscopy and density functional theory calculations. Different supramolecular structures have been observed depending on molecular coverage and annealing. In the low coverage regime, flat lying deprotonated species are formed which give way to benzotriazolate molecules in an upright configuration by increasing the BTAH exposure. The ensuing monolayer is self-limiting but, upon annealing above 150 °C, transforms into a highly ordered nano-ridge structure resulting from a significant in-plane and out-of-plane reconstruction of the surface. All structures are characterised by a strong molecule–substrate interaction and the high coverage phases are dominated by the formation of metal–organic complexes between copper adatoms and benzotriazolate species. These findings shed light on the nature and strength of the interaction occurring between BTAH and copper which lies at the basis of the effectiveness of this prototypical corrosion inhibitor.

Shedding Light on the Interfacial Structure of Low-Coverage Alkanethiol Lattices

A comprehensive description of the self-assembly process of alkanethiols on Au(111) is presented, focused on the initial formation of the lying down phases. Low-coverage monolayers are prepared by the disintegration of Au144(RS)60 nanoclusters on the reconstructed (22 × ?3)-Au(111) surface. The method provides a limited number of thiols together with a large excess of gold adatoms. Scanning tunneling microscopy and density functional theory calculations were employed to study the transition between low to high thiolate coverage phases. The process involves different lattices and surface transformations, including thiyl radicals on the herringbone reconstruction, radical-induced herringbone lifting, and the formation of energetically similar metastable phases formed by RS-Au-RS moieties. Results also show that the transition is slow, and different surface structures can coexist on the same sample. Along the process, the first source of Au adatoms to form the RS-Au-SR moieties is the lifting of the herringbone reconstruction because of the lower energetic cost to extract the extra Au atom. However, for hexanethiol (and shorter alkanethiols) at low coverage, additional Au adatoms must be taken from terraces leading to vacancy islands. This process can be entirely suppressed by growing the lying down phases in the presence of an excess of Au adatoms. Taken together, our results shed light on the elusive initial steps of thiol adsorption on clean reconstructed Au, showing that the RS-Au-SR staple motif is also present at the interface of low-coverage self-assembled monolayers.

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.

Determining multiallelic complex copy number and sequence variation from high coverage exome sequencing data.

BackgroundCopy number variation (CNV) is a major component of genomic variation, yet methods to accurately type genomic CNV lag behind methods that type single nucleotide variation. High-throughput sequencing can contribute to these methods by using sequence read depth, which takes the number of reads that map to a given part of the reference genome as a proxy for copy number of that region, and compares across samples. Furthermore, high-throughput sequencing also provides information on the sequence differences between copies within and between individuals.MethodsIn this study we use high-coverage phase 3 exome sequences of the 1000 Genomes project to infer diploid copy number of the beta-defensin genomic region, a well-studied CNV that carries several beta-defensin genes involved in the antimicrobial response, signalling, and fertility. We also use these data to call sequence variants, a particular challenge given the multicopy nature of the region.ResultsWe confidently call copy number and sequence variation of the beta-defensin genes on 1285 samples from 26 global populations, validate copy number using Nanostring nCounter and triplex paralogue ratio test data. We use the copy number calls to verify the genomic extent of the CNV and validate sequence calls using analysis of cloned PCR products. We identify novel variation, mostly individually rare, predicted to alter amino-acid sequence in the beta-defensin genes. Such novel variants may alter antimicrobial properties or have off-target receptor interactions, and may contribute to individuality in immunological response and fertility.ConclusionsGiven that 81 % of identified sequence variants were not previously in dbSNP, we show that sequence variation in multiallelic CNVs represent an unappreciated source of genomic diversity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2123-y) contains supplementary material, which is available to authorized users.

A model for the catalytic oxidation of CO that includes CO desorption and diffusion, O repulsion, and impurities in the gas phase

We present kinetic Monte Carlo simulations exploring the nonequilibrium phase diagram of a modified Ziff–Gulari–Barshad (ZGB) dynamic lattice-gas model for the catalytic oxidation of carbon monoxide (CO) on a surface. The modified model includes the simultaneous presence of contaminants in the gas phase, CO desorption, CO diffusion, and strong repulsion between adsorbed oxygen (O) atoms; all of which have been observed in experimental systems. We find that the strong O–O repulsion produces higher reaction rates, albeit in a reduced reactive pressure window. In systems with impurities, the CO2 production rate is greatly reduced, but this effect is mitigated by CO desorption and diffusion. CO desorption has the effect of widening the reactive pressure window, while CO diffusion has the effect of increasing the reaction rate. In some parameter regimes the presence of impurities destroys the discontinuous transition between the reactive and high CO coverage phases.

First-order phase transition during displacement of amphiphilic biomacromolecules from interfaces by surfactant molecules

The adsorption of surfactants onto a hydrophobic interface, already laden with a fixed number of amphiphilic macromolecules, is studied using the self consistent field calculation method of Scheutjens and Fleer. For biopolymers having unfavourable interactions with the surfactant molecules, the adsorption isotherms show an abrupt jump at a certain value of surfactant bulk concentration. Alternatively, the same behaviour is exhibited when the number of amphiphilic chains on the interface is decreased. We show that this sudden jump is associated with a first-order phase transition, by calculating the free energy values for the stable and the metastable states at both sides of the transition point. We also observe that the transition can occur for two approaching surfaces, from a high surfactant coverage phase to a low surfactant coverage one, at sufficiently close separation distances. The consequence of this finding for the steric colloidal interactions, induced by the overlap of two biopolymer + surfactant films, is explored. In particular, a significantly different interaction, in terms of its magnitude and range, is predicted for these two phases. We also consider the relevance of the current study to problems involving the competitive displacement of proteins by surfactants in food colloid systems.

High temperature growth of Ag phases on Ge(111)

The growth of the (3 × 1) and (√3 × √3)R30° phases of Ag on Ge(111) on substrates at temperatures from 540 to 660 °C is characterized with low energy electron microscopy (LEEM) and low energy electron diffraction (LEED). From 540 °C to the Ag desorption temperature of 575 °C, LEEM images show that growth of the (3 × 1) phase begins at step edges. Upon completion of the (3 × 1) phase, the (√3 × √3)R30° phase is observed with a dendritic growth morphology that is not much affected by steps. For sufficiently high deposition rates, Ag accumulates on the sample above the desorption temperature. From 575 to 640 °C, the growth proceeded in a manner similar to that at lower temperatures, with growth of the (3 × 1) phase to completion, followed by growth of the (√3 × √3)R30° phase. Increasing the substrate temperature to 660 °C resulted in only (3 × 1) growth. In addition, for samples with Ag coverage less than 0.375ML, LEEM and LEED images were used to follow a reversible phase transformation near 575 °C, between a mixed high coverage phase of [(4 × 4) + (3 × 1)] and the high temperature, lower coverage (3 × 1) phase.

Dissociative Hydrogen Adsorption on Close-Packed Cobalt Nanoparticle Surfaces

The dissociative adsorption of hydrogen on cobalt is central to a number of catalytic reactions, yet to date there are relatively few studies examining this important process. Here we utilize Co nanoparticles grown on Cu(111), instead of the traditional planar Co single crystals, to study a more catalytically relevant form of Co. We present scanning tunneling microscopy images of different phases of H on the close-packed Co nanoparticle surfaces with a range of densities. Our data reveal a so-far unreported high coverage phase of H with a (1 × 1) structure and elucidate the importance of spillover from step edges in H adsorption. We also illustrate that, in contrast to the low density phases, the H-(1 × 1) structure can only be formed at an intermediate temperature, indicating that compression to this higher-density phase is activated. Density functional theory calculations yield energies for each of the H overlayer structures, as well as their preferred geometries. This work is the first to report on higher coverage (>0.75 ML) phases of H on Co, which are undoubtedly important in catalytic systems at elevated pressure. Finally, through the use of epitaxial Co nanoparticle growth on Cu(111), we illustrate the importance of step edges in H2 activation and the formation of dense H phases.

Adsorption of α,β-Unsaturated Aldehydes on Pt(111) and Pt−Sn Alloys: II. Crotonaldehyde

By employing high-resolution electron energy loss spectroscopy (HREELS), temperature-programmed desorption (TPD), and low-energy electron diffraction (LEED), we have studied the adsorption and thermal decomposition of crotonaldehyde (2-butenal) on Pt(111) as well as Pt3Sn/Pt(111) and Pt2Sn/Pt(111) surface alloys. In order to understand the adsorption structures and the vibrational properties, an extensive theoretical study of the possible adsorption geometries and vibrational spectra on the three considered surfaces has been carried out using density functional theory (DFT). A careful analysis of the variety of possible adsorption configurations of crotonaldehyde allowed structural identification by correlating their vibrational fingerprints with the measured HREELS peaks. The mixed phases of crotonaldehyde formed on the model catalysts turned out to be even more complex than those we found in previous studies for prenal. The set of stable configurations identified by combination of HREELS with DFT consists of η2, η3, and η4 flat adsorption structures, which exhibit adsorption energies from −69 to −80 kJ/mol. Nonetheless, the thermal decomposition measured with TPD and the general adsorption behavior show similarities to prenal and acrolein. Starting from a strongly adsorbed state on Pt(111) at low temperatures, crotonaldehyde decomposes at temperatures close to 300 K. On the surface alloys, a high-coverage phase with structures of low hapticity such as η2-diσ(CC) is measured at low temperatures (∼160 K), and a low-coverage situation of high hapticity η2, η3, and η4 configurations is formed at higher temperatures (∼200 K). On Pt3Sn/Pt(111), two energetically competitive η1-top-E-(s)-trans-OSn forms cannot be excluded at low temperatures.

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.

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.

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.

Decay of metastable phases in a model for the catalytic oxidation of CO

We study by kinetic Monte Carlo simulations the dynamic behavior of a Ziff-Gulari-Barshad model with CO desorption for the reaction CO + O-->CO(2) on a catalytic surface. Finite-size scaling analysis of the fluctuations and the fourth-order order-parameter cumulant show that below a critical CO desorption rate, the model exhibits a nonequilibrium first-order phase transition between low and high CO coverage phases. We calculate several points on the coexistence curve. We also measure the metastable lifetimes associated with the transition from the low CO coverage phase to the high CO coverage phase, and vice versa. Our results indicate that the transition process follows a mechanism very similar to the decay of metastable phases associated with equilibrium first-order phase transitions and can be described by the classic Kolmogorov-Johnson-Mehl-Avrami theory of phase transformation by nucleation and growth. In the present case, the desorption parameter plays the role of temperature, and the distance to the coexistence curve plays the role of an external field or supersaturation. We identify two distinct regimes, depending on whether the system is far from or close to the coexistence curve, in which the statistical properties and the system-size dependence of the lifetimes are different, corresponding to multidroplet or single-droplet decay, respectively. The crossover between the two regimes approaches the coexistence curve logarithmically with system size, analogous to the behavior of the crossover between multidroplet and single-droplet metastable decay near an equilibrium first-order phase transition.

The crystalline structures of the even alkanes hexane, octane, decane, dodecane and tetradecane monolayers adsorbed on graphite at submonolayer coverages and from the liquidElectronic Supplementary Information available. See http://www.rsc.org/suppdata/cp/b1/b108190j/

Neutron and X-ray diffraction have been used to structurally characterise the crystalline monolayer structures of hexane, octane, decane, dodecane and tetradecane adsorbed on graphite at sub-monolayer coverages and when coexisting with liquid alkane. The structures of all the molecules investigated at both coverages and low temperatures are isomorphous with rectangular unit cells of plane group pgg containing two molecules per cell. In both high- and low-coverage structures the molecules have their extended axes parallel to the surface. The plane of the carbon skeleton is found to be parallel to the graphite surface. The monolayers at sub-monolayer coverages are interpreted as uniaxially commensurate while those monolayers coexisting with the liquid are fully commensurate. Dodecane and tetradecane are exceptional: dodecane forms additional phases at high temperatures just prior to melting, at both low and high coverages. In these structures the molecules in the unit cell are parallel to each other with plane group cmm. Tetradecane only forms a single phase at high coverages in which the molecules appear to be parallel and upright, similar to the dodecane high temperature, high coverage phase.

Quantitative structural determination of the high coverage phase of the benzoate species on Cu(1 1 0)

The local adsorption site and molecular orientation of the benzoate species adsorbed on Cu(1 1 0) at 330 K have been determined using O1s scanned-energy mode photoelectron diffraction. The molecule was found to interact with the surface via the carboxylate group, giving a Cu–O bond length of 1.91 Å. The molecules occupy the short bridge sites (the O atoms being slightly displaced from atop sites) and are aligned along the [ 1 ̄ 1 0] azimuth with the molecular plane oriented perpendicular to the surface.

Coadsorption of water and CO molecules on Ru(0 0 1) at high CO coverages: comparisons with a Ru(0 0 1) electrode surface

The coadsorption of carbon monoxide (CO) and water molecules on a Ru(0 0 1) surface has been studied by infrared spectroscopy, LEED and STM. At high CO coverage phases, a 2×2-(2CO+D 2O) structure was observed on both UHV and electrode surfaces. Electrode potential dependent structures from CO and water adlayers on an electrode surface were reproduced on a UHV surface by controlling molecular orientations of the first layer and second over-layer water molecules. At lower CO coverages, a CO band center showed coverage dependent shift down to 1444 cm −1 due to an electron transfer from a lone pair of a water molecule to CO 2π *.

Improvement of Gas Chromatographic Performance of Cyclic Siloxane Bonded Phases by Incorporation of n-Alkyl Groups

Cyclic siloxane-based silica columns of high retention capacity for light hydrocarbons were prepared by incorporation of octyl and octadecyl groups on the siloxane skeleton. Spectroscopic studies revealed the presence of the alkyl groups on the silica surface, which results in high surface coverage of the packing materials. The retention characteristics of the columns are significantly higher than those of cyclic siloxane phases due to their high surface coverage and better solute-stationary phase interactions. In agreement with previous data for micropacked columns, the H vs ū curves, on passing through the optimum region, remained substantially constant at high linear gas velocities, indicating their usefulness for fast analysis of light hydrocarbons at high flow rates without any appreciable loss in column performance. Presumably due to greater availability of the bonded alkyl groups for interactions, a 10-component mixture of C(1)-C(4) saturated and unsaturated hydrocarbons was sufficiently separated on the hexamethylcyclotrisiloxane-octadecylsilyl phase compared to the conventional octadecyldimethylsilyl phase, irrespective of the high carbon content of the latter.

Use of x-ray reflectivity for determining the Si(111) sqrt 3 x sqrt 3-Bi surface structures.

Absolute reflectivities of x-rays from the Si(111)\ensuremath{\surd}3\ifmmode\times\else\texttimes\fi{}\ensuremath{\surd}3-Bi surface were measured along the 00 and 12\ifmmode\bar\else\textasciimacron\fi{} reciprocal-lattice rods. Two phases of the surface, a low-coverage phase and a high-coverage phase, were recognized from the reflectivity measurement. The Bi coverages of the two phases were determined as 1 ML and 1/3 ML. The 1-ML phase takes the milk stool structure. For the 1/3-ML phase the adsorbed Bi atom is found to be on the ${\mathit{T}}_{4}$ site and the distance between the Bi layer and the first Si layer is 1.60 \AA{}. For data analysis, expressions of the absolute reflectivities obtained by a newly developed dynamical theory are used.