The decomposition of methanol-d4 (CD3OD) on Rh nanoclusters grown by the deposition of Rh vapors onto an ordered thin film of Al2O3/NiAl(100) was studied, with various surface-probe techniques and largely under near-ambient-pressure (NAP) conditions. The results showed a superior reactivity of small Rh clusters (diameter < 1.5 nm) exposed to CD3OD at 5 × 10-3-0.1 mbar at 400 K; the gaseous production of CO and D2 from decomposed methanol-d4 per Rh surface site on the small Rh clusters with diameters of â¼1.1 nm was nearly 8 times that on large ones with diameters of â¼3.5 nm. The promotion of reactivity with decreased cluster size under NAP conditions was evidently greater than that under ultrahigh vacuum conditions. Moreover, the concentration of atomic carbon (C*; where * denotes adsorbate)-a key catalyst poisoner-yielded from the dissociation of CO* from dehydrogenated methanol-d4 was significantly smaller on small clusters (diameter < 1.5 nm). The NAP size effect on methanol-d4 decomposition involved the surface hydroxyl (OH*) from the little co-adsorbed water (H2O*) that was dissociated at a probability dependent on the cluster size. H2O* was more likely dissociated into OH* on small Rh clusters, by virtue of their more reactive d-band structure, and the OH* then effectively promoted the O-D cleavage of methanol-d4, as the rate-determining step, and thus the reaction probability; on the other hand, the OH* limited CO* dissociation on small Rh clusters via both adsorbate and lateral effects. These results suggest that the superior properties of small Rh clusters in both reactivity and anti-poisoning would persist and be highly applicable under "real-world" catalysis conditions.
Transition metal dichalcogenides, by virtue of their two-dimensional structures, could provide the largest active surface for reactions with minimal materials consumed, which has long been pursued in the design of ideal catalysts. Nevertheless, their structurally perfect basal planes are typically inert; their surface defects, such as under-coordinated atoms at the surfaces or edges, can instead serve as catalytically active centers. Here we show a reaction probability > 90 % for adsorbed methanol (CH3OH) on under-coordinated Pt sites at surface Te vacancies, produced with Ar+ bombardment, on layered PtTe2 - approximately 60 % of the methanol decompose to surface intermediates CHxO (x = 2, 3) and 35 % to CHx (x = 1, 2), and an ultimate production of gaseous molecular hydrogen, methane, water and formaldehyde. The characteristic reactivity is attributed to both the triangular positioning and varied degrees of oxidation of the under-coordinated Pt at Te vacancies.
We have studied the decomposition of methanol-d4 on thin film Al2O3/NiAl(100) under near-ambient-pressure conditions, with varied surface-probe techniques and calculations based on density-functional theory. Methanol-d4 neither adsorbed nor reacted on Al2O3/NiAl(100) at 400 K under ultrahigh vacuum conditions, whereas they dehydrogenated, largely to methoxy-d3 (CD3O*, * denoting adsorbates) and formaldehyde-d2 (CD2O*), on the surface when the methanol-d4 partial pressure was increased to 10-3 mbar and above. The dehydrogenation was facilitated by hydroxyl (OH* or OD*) from the dissociation of little co-adsorbed water; a small fraction of CD2O* interacted further with OH* (OD*) to form, via intermediate CD2OOH* (CD2OOD*), formic acid (DCOOH* or DCOOD*). A few surface carbonates were also yielded, likely on the defect sites of Al2O3/NiAl(100). The results suggest that alumina not only supports metal clusters but also participates in reactions under realistic catalytic conditions. One may consider accordingly the multiple functions of alumina while designing ideal catalysts.
Layered transition metal dichalcogenides (TMDs) are two-dimensional materials exhibiting a variety of unique features with great potential for electronic and optoelectronic applications. The performance of devices fabricated with mono or few-layer TMD materials, nevertheless, is significantly affected by surface defects in the TMD materials. Recent efforts have been focused on delicate control of growth conditions to reduce the defect density, whereas the preparation of a defect-free surface remains challenging. Here, we show a counterintuitive approach to decrease surface defects on layered TMDs: a two-step process including Ar ion bombardment and subsequent annealing. With this approach, the defects, mainly Te vacancies, on the as-cleaved PtTe2 and PdTe2 surfaces were decreased by more than 99%, giving a defect density <1.0 × 1010 cm-2, which cannot be achieved solely with annealing. We also attempt to propose a mechanism behind the processes.
We studied the dissociation of water (H2O*, with * denoting adspecies) on atomic oxygen (O*)-covered Rh nanoclusters (RhO* ) supported on a graphene film grown on a Ru(0001) surface [G/Ru(0001)] under ultrahigh-vacuum conditions and with varied surface-probe techniques and calculations based on density-functional theory. The graphene had a single rotational domain; its lattice expanded by about 5.7% to match the Ru substrate structurally better. The Rh clusters were grown by depositing Rh vapors onto G/Ru(0001); they had an fcc phase and grew in (111) orientation. Water adsorbed on the Rh clusters was dissociated exclusively in the presence of O*, like that on a Rh(111) single-crystal surface. Contrary to the case on Rh(111)O* , excess O* (even at a saturation level) on small RhO* clusters (diameter of 30-34 Å) continued to promote, instead of inhibiting, the dissociation of water; the produced hydroxyl (OH*) increased generally with the concentration of O* on the clusters. The difference results from more reactive O* on the RhO* clusters. O* on RhO* clusters activated the dissociation via both the formation of hydrogen bonds with H2O* and abstraction of H directly from H2O*, whereas O* on Rh(111)O* assisted the dissociation largely via the formation of hydrogen bonds, which was readily obstructed with an increased O* coverage. As the disproportionation (2 OH* â H2O* + O*) is endothermic on the RhO* clusters but exothermic on Rh(111)O* , OH* produced on RhO* clusters showed a thermal stability superior to that on the Rh(111)O* surface-thermally stable up to 400 K.
The size effect on the activity of a catalyst has been a focal issue since ideal catalysts were pursued, whereas that on the degradation of a catalyst, by reaction intermediates such as CO, is little discussed. We demonstrate that the dehydrogenation of methanol-d4 on supported Rh nanoclusters precovered with CO (Rh-CO clusters) was obstructed, indicated by a decreased production of CO and D2; the obstructive effect exhibits a remarkable dependence on the cluster size, with a minimum at a cluster diameter near 1.4 nm. The decreased production arose from a decreased reaction probability controlled by the increased activation energy for each dehydrogenation step (including formation of methoxy-d3), adsorption energies of CO, and repulsion from the CO array on the Rh-CO surface. The effects of these factors in deactivating the clusters varied separately with the cluster size. Consequently, the size effect on the CO poisoning should be taken into account in engineering the cluster size to optimize the catalytic performance.
DNA methylation is an important epigenetic regulator in gene expression and has several roles in cancer and disease progression. MethHC version 2.0 (MethHC 2.0) is an integrated and web-based resource focusing on the aberrant methylomes of human diseases, specifically cancer. This paper presents an updated implementation of MethHC 2.0 by incorporating additional DNA methylomes and transcriptomes from several public repositories, including 33 human cancers, over 50 118 microarray and RNA sequencing data from TCGA and GEO, and accumulating up to 3586 manually curated data from >7000 collected published literature with experimental evidence. MethHC 2.0 has also been equipped with enhanced data annotation functionality and a user-friendly web interface for data presentation, search, and visualization. Provided features include clinical-pathological data, mutation and copy number variation, multiplicity of information (gene regions, enhancer regions, and CGI regions), and circulating tumor DNA methylation profiles, available for research such as biomarker panel design, cancer comparison, diagnosis, prognosis, therapy study and identifying potential epigenetic biomarkers. MethHC 2.0 is now available at http://awi.cuhk.edu.cn/â¼MethHC.
Biomarkers, Tumor/genetics , DNA Methylation , Databases, Genetic , Epigenesis, Genetic , Gene Expression Regulation, Neoplastic , Neoplasms/genetics , Biomarkers, Tumor/metabolism , Circulating Tumor DNA/blood , Circulating Tumor DNA/genetics , DNA Copy Number Variations , Disease Progression , Enhancer Elements, Genetic , High-Throughput Nucleotide Sequencing , Humans , Internet , Microarray Analysis , Molecular Sequence Annotation , Mutation , Neoplasms/classification , Neoplasms/diagnosis , Neoplasms/metabolism , Software , Transcriptome
Annealed Rh nanoclusters on an ordered thin film of Al2O3/NiAl(100) were shown to exhibit a promoted reactivity toward the decomposition of methanol-d4, under both ultrahigh vacuum and near-ambient-pressure conditions. The Rh clusters were grown with vapor deposition onto the Al2O3/NiAl(100) surface at 300 K and annealed to 700 K. The decomposition of methanol-d4 proceeded only through dehydrogenation, with CO and deuterium as products, on Rh clusters both as prepared and annealed. Nevertheless, the catalytic reactivity of the annealed clusters, measured with the production of either CO or deuterium per surface Rh site from the reaction, became at least 2-3 times that of the as-prepared ones. The promoted reactivity results from an altered support effect associated with an annealing-induced mass transport at the surface. Our results demonstrate a possibility to practically prepare reactive Rh clusters, regardless of the cluster size, that can tolerate an elevated reaction temperature, with no decreased reactivity.
We have studied the reforming reaction of ethanol co-adsorbed with atomic oxygen (O*, * denotes adspecies) and deuterated water (D2O*) on a Rh(111) surface, with varied surface probe techniques under UHV conditions and with density-functional-theory calculations. Adsorbed ethanol molecules were found to penetrate readily through pre-adsorbed water, even up to eight overlayers, to react at the Rh surface; they decomposed at a probability promoted by the water overlayers. The production probabilities of H2, CO, CH2CH2 and CH4 continued to increase with co-adsorbed D2O*, up to two D2O overlayers, despite separate increasing rates; above two D2O overlayers, those of H2, CO and CH2CH2 were approximately saturated while that of CH4 decreased. The increased (or saturated) production probabilities are rationalized with an increased (saturated) concentration of surface hydroxyl (OD*, formed by O* abstracting D from D2O*), whose intermolecular hydrogen bonding with adsorbed ethanol facilitates proton transfer from ethanol to OD* and thus enhances the reaction probability. The decreasing behavior of CH4 could also involve the competition for H* with the formation of H2 and HDO.
MicroRNAs (miRNAs) are small non-coding RNAs (typically consisting of 18-25 nucleotides) that negatively control expression of target genes at the post-transcriptional level. Owing to the biological significance of miRNAs, miRTarBase was developed to provide comprehensive information on experimentally validated miRNA-target interactions (MTIs). To date, the database has accumulated >13,404 validated MTIs from 11,021 articles from manual curations. In this update, a text-mining system was incorporated to enhance the recognition of MTI-related articles by adopting a scoring system. In addition, a variety of biological databases were integrated to provide information on the regulatory network of miRNAs and its expression in blood. Not only targets of miRNAs but also regulators of miRNAs are provided to users for investigating the up- and downstream regulations of miRNAs. Moreover, the number of MTIs with high-throughput experimental evidence increased remarkably (validated by CLIP-seq technology). In conclusion, these improvements promote the miRTarBase as one of the most comprehensively annotated and experimentally validated miRNA-target interaction databases. The updated version of miRTarBase is now available at http://miRTarBase.cuhk.edu.cn/.
Databases, Nucleic Acid , MicroRNAs/metabolism , Circulating MicroRNA/metabolism , Data Mining , Gene Expression Regulation , RNA, Messenger/metabolism , User-Computer Interface
Pt and Rh nanoclusters, grown on deposition of Pt and Rh vapors onto graphene/Pt(111), show separate reactivity toward the decomposition of methanol-d4. The Pt (Rh) clusters had a mean diameter 2.0-3.5 nm (2.1-4.0 nm) and height 0.45-0.94 nm (0.41-0.9 nm) evolving with the coverage; they were structurally ordered, having an fcc phase and growing in (111) orientation, and had lattice constants similar to their bulk values. Methanol-d4 on the Pt clusters did not decompose but desorbed mostly, disparate from that on Pt(111) surface; the disparity arose as the adsorption energies of methanol-d4 on most surface sites of the Pt clusters became smaller than their single crystal counterpart. This size effect, nevertheless, did not apply on the Rh clusters, despite their similar atomic stacking; the Rh clusters showed a reactivity similar to that of the Rh(111) surface because the adsorption energies of methanol-d4 on both Rh clusters and Rh(111) are comparable. The distinct size dependence was rationalized through their electronic structures and charge distribution of Fukui function mapping. Our results suggest that reactive transition metals do not necessarily become more reactive while they are scaled down to nanoscale; their reactivity evolves with their size in a manner largely dependent on their electronic nature.
The decomposition of methanol-d4 that was adsorbed on Au-Rh bimetallic nanoclusters grown by the sequential deposition of Au and Rh vapors onto ordered thin-film Al2O3/NiAl(100) at 300 K, occurred by means of dehydrogenation and primarily on the surface Rh. Nevertheless, the surface Rh atoms were not equally reactive; their reactivity altered with both structural and electronic effects arising from the alloying. The Au deposited on Rh clusters decorated the surface and deactivated Rh by not only directly obstructing them but also by neighboring them. As the initially incorporated Au tended to aggregate around reactive low-coordinated Rh atoms, such as corner Rh atoms, the reactivity of the cluster, indicated by the CO and deuterium (D2) produced per surface Rh, decreased markedly. In contrast, the Rh deposited on Au clusters promoted their reactivity. The reactivity was sharply enhanced by a few incorporated Rh atoms, as they preferentially decorated the edge Au atoms, resulting in their lower coordination, more positive charge, higher energetic d-band centers, and high reactivity. On the reactive Rh, the scission of the O-D bond in the initial dehydrogenation of methanol-d4 became more preferential than the competing desorption. The further incorporated Rh failed to promote the reactivity, but the clusters remained more reactive than those formed by Rh clusters incorporating Au as their structuring involved an active atomic segregation that yielded more low-coordinated and reactive surface Rh.
The dissociation of water molecules absorbed on a cleaved non-polar GaN(11[combining macron]00) surface was studied primarily with synchrotron-based photoemission spectra and density-functional-theory calculations. The adsorbed water molecules are spontaneously dissociated into hydrogen atoms and hydroxyl groups at either 300 or 130 K, which implies a negligible activation energy (<11 meV) for the dissociation. The produced H and OH were bound to the surface nitrogen and gallium on GaN(11[combining macron]00) respectively. These results highlight the promising applications of the non-polar GaN(11[combining macron]00) surface in water dissociation and hydrogen generation.
With calculations based on density-functional theory (DFT) we investigated the adsorption of a single Au atom and a dimer on thin θ-Al2O3(001) films supported on NiAl(100). The interaction of the Au adsorbates with the surface was shown to depend on the thickness of the film. The adsorption energy for an Au atom on θ-Al2O3(001)/NiAl(100) of film thickness ≤four atomic layers was significantly enhanced-over three times that on a bulk θ-Al2O3(001) surface, and accompanied with a shortened Au-oxide bond and an uplifted Au-binding Al. The strong Au-surface interaction involved a decreased work function of θ-Al2O3(001)/NiAl(100) and consequently drove charge to transfer from the substrate to the adsorbed Au atom; the charge was transferred from NiAl, through alumina, on monolayer θ-Al2O3(001)/NiAl(100), but directly from alumina on thicker layers. For an Au dimer, both upright (end-on) and flat-lying (side-on) geometries existed. The flat-lying dimer was preferred on mono- and tri-layer alumina films, having a greater adsorption energy but a weakened Au-Au bond, whereas the upright geometry prevailed for films of other thickness, having a weaker adsorption energy and being less charged, similar to that on a bulk θ-Al2O3(001) surface. The results imply an opportunity to control the properties and morphologies of metal clusters supported on an oxide film by tuning its thickness.
The surface structures and compositions of Au-Rh bimetallic nanoclusters on an ordered thin film of Al2O3/NiAl(100) were investigated, primarily with infrared reflection absorption spectra and temperature-programmed desorption of CO as a probe molecule under ultrahigh-vacuum conditions and calculations based on density-functional theory. The bimetallic clusters were formed by sequential deposition of vapors of Au and Rh onto Al2O3/NiAl(100) at 300 K. Alloying in the clusters was active and proceeded toward a specific structure-a fcc phase, (100) orientation, and Rh core-Au shell structure, regardless of the order of metal deposition. For Au clusters incorporating deposited Rh, the Au atoms remained at the cluster surface through position exchange and became less coordinated; for deposition in reverse order, deposited Au simply decorated the surfaces of Rh clusters. Both adsorption energy and infrared absorption intensity were enhanced for CO on Au sites of the bimetallic clusters; both of them are associated with the bonding to Rh and also a decreased coordination number of CO-binding Au. These enhancements can thus serve as a fingerprint for alloying and atomic inter-diffusion in similar bimetallic systems.
Self-organized alloying of Au with Rh in nanoclusters on an ordered thin film of Al2O3/NiAl(100) was investigated via various surface probe techniques under ultrahigh-vacuum conditions and calculations based on density-functional theory. The bimetallic clusters were formed on the sequential deposition of vapors of Au and Rh onto Al2O3/NiAl(100) at 300 K. The formation was more effective on the oxide seeded with Rh, since all post-deposited Au joined the pregrown Rh clusters; for metal deposition in the reverse order, some separate Rh clusters were formed. The contrasting behavior is rationalized through the easier nucleation of Rh on the oxide surface, due to the stronger Rh-oxide and Rh-Rh bonds. The alloying in the clusters proceeded, regardless of the order of metal deposition, toward a specific structure: an fcc phase, (100) orientation and Rh core-Au shell structure. The orientation, structural ordering and lattice parameters of the Au-Rh bimetallic clusters resembled Rh clusters, rather than Au clusters, on Al2O3/NiAl(100), even with Rh in a minor proportion. The Rh-predominated core-shell structuring corresponds to the binding energies in the order Rh-Rh > Rh-Au > Au-Au. The core-shell segregation, although active, was somewhat kinetically hindered, since elevating the sample temperature induced further encapsulation of Rh. The bimetallic clusters became thermally unstable above 500 K, for which both Rh and Au atoms began to diffuse into the substrate. Moreover, the electronic structures of surface elements on the bimetallic clusters, controlled by both structural and electronic effects, show a promising reactivity.
With a variety of surface probe techniques, we investigated low-temperature decomposition of methanol on Au nanoclusters formed by vapor deposition onto an ordered Al(2)O(3)/NiAl(100) thin film. Upon adsorption of methanol on the Au clusters (with mean diameter 1.5-3.8 nm and height 0.45-0.85 nm) at 110 K, some of the adsorbed methanol dehydrogenates directly into carbon monoxide (CO); the produced hydrogen atoms (H) begin to desorb near 125 K whereas most of the CO desorbs above 240 K. The reaction exhibits a significant dependence on the Au coverage: the produced CO increases in quantity with the Au coverage, reaches a maximum at about 1.0-1.5 ML Au, whereas decreases with further increase of the Au coverage. The coverage-dependence is rationalized partly by an altered number of reactive sites associated with low-coordinated Au in the clusters. At least two kinds of reactive sites for the low-temperature decomposition are distinguished through distinct C-O stretching frequencies (2050 cm(-1) and 2092 cm(-1)) while the produced CO co-adsorbs with H and methanol.
Au-Pt bimetallic nanoclusters on a thin film of Al(2)O(3)/NiAl(100) undergo significant structural evolution on variation of the temperature. Au and Pt deposited sequentially from the vapor onto thin-film Al(2)O(3)/NiAl(100) at 300 K form preferentially bimetallic nanoclusters (diameter ⦠6.0 nm and height ⦠0.8 nm) with both Au and Pt coexisting at the cluster surface, despite the order of metal deposition. These bimetallic clusters are structurally ordered, have a fcc phase and grow with their facets either (111) or (001) parallel to the θ-Al(2)O(3)(100) surface. Upon annealing the clusters to 400-500 K, the Au atoms inside the clusters migrate toward the surface, resulting in formation of a structure with a Pt core and an Au shell. Annealing the sample to 500-650 K reorients the bimetallic clusters--all clusters have their (001) facets parallel to the oxide surface--and induces oxidation of Pt. Such annealed bimetallic clusters become encapsulated with the aluminium-oxide materials and a few Au remain on the surface.
