3-fold Sites Research Articles

Strong purifying selection in haploid tissue-specific genes of Scots pine supports the masking theory.

The masking theory states that genes expressed in haploid stage will be under more efficient selection. In contrast, selection will be less efficient in genes expressed in diploid stage, where the fitness effects of recessive deleterious or beneficial mutations can be hidden from selection in heterozygous form. This difference can influence several evolutionary processes such as the maintenance of genetic variation, adaptation rate, and genetic load. Masking theory expectations have been confirmed in single-cell haploid and diploid organisms. However, in multicellular organisms, such as plants, the effects of haploid selection are not clear-cut. In plants, the great majority of studies indicating haploid selection have been carried out using male haploid tissues in angiosperms. Hence, evidence in these systems is confounded with the effects of sexual selection and intra-specific competition. Evidence from other plant groups is scarce and results show no support for the masking theory. Here we have used a gymnosperm Scots pine megagametophyte, a maternally-derived seed haploid tissue, and four diploid tissues to test the strength of purifying selection on a set of genes with tissue-specific expression. By using targeted resequencing data of those genes, we obtained estimates of genetic diversity, the site frequency spectrum of 0-fold and 4-fold sites, and inferred the distribution of fitness effects (DFE) of new mutations in haploid and diploid tissue-specific genes. Our results show that purifying selection is stronger for tissue-specific genes expressed in the haploid megagametophyte tissue, and that this signal of strong selection is not an artifact driven by high expression levels.

Understanding the agglomerate crystallisation of hexamine through X-ray microscopy and crystallographic modelling

The detailed molecular-scale mechanism of the growth of organic crystals underpins a diversity of phenomena, such as the isolation and purification of high-quality materials for the pharmaceutical and fine chemical sectors. Recent advances in X-ray Microscopy (XRM) and complementary diffraction contrast tomography (DCT) have enabled the detailed characterisation of the micro-structure of hexamine agglomerates. Detailed XRM analysis of the growth history and micro-structure of such agglomerates reveals a highly orientated epitaxial inter-relationship between their constituent micro-crystallites. This is found to be consistent with a secondary nucleation growth mechanism associated with re-growth at the 3-fold corner sites within the crystals’ dominant {110} dodecahedral morphology. The agglomeration appears to heal upon further growth as the aligned agglomerated micro-crystals connect and fuse together but, in doing so, pockets of inter-crystallite mother liquor become trapped forming a symmetric pattern of solvent inclusions. The mechanistic origin of this phenomenon is rationalised with respect to historical data together with an analysis of the solid-state chemistry of the compound through the development of a ‘snow flake’ model. The latter draws upon hexamine’s propensity for edge growth instabilities with increasing crystal size as well as its tendency for unstable growth at the facet corners along the 〈111〉 directions, a situation compounded by the lack of growth-promoting dislocations at the centers of the {110} habit surfaces. The agglomerative mechanism presented here could apply to other high symmetry crystal systems, particularly those whose crystal structures involve centred Bravais lattices and where the dominant inter-molecular interactions are angled towards the facet edges.

Investigating the CO activation mechanism on hcp-Fe7C3 (211) via density functional theory

The Fischer-Tropsch to Olefins (FTO) process over iron catalysts has attracted interests of academia due to its promising catalytic performance. Several iron carbides phases have been discovered in the spent iron catalysts. Recently, the hcp-Fe7C3 phase was reported to be active in the FTO process. Hence, to figure out how the hcp-Fe7C3 works in the FTO process, DFT calculations were performed to investigate the CO activation mechanism first. It was found that the top site and 4-fold site are the major adsorption sites for CO. The surface carbon is able to be the CO activation site by CO insertion dissociation pathway. The effective barrier energy of the preferred CO insertion dissociation pathway is 1.48 eV. The CO could also be activated on the top site through H-assist CO dissociation pathway or the 4-fold site through direct CO dissociation pathway with the effective barrier energy of 1.30 eV and 1.18 eV, respectively. Compared the effective barrier energy of CO activation mechanism on the hcp-Fe7C3 (211) with those on other iron carbides, the hcp-Fe7C3 (211) is thought to be high active on the CO activation process under the FTO condition.

A Study of Faster-Z Evolution in the Great Tit (Parus major).

Sex chromosomes contribute substantially to key evolutionary processes such as speciation and adaptation. Several theories suggest that evolution could occur more rapidly on sex chromosomes, but currently our understanding of whether and how this occurs is limited. Here, we present an analysis of the great tit (Parus major) genome, aiming to detect signals of faster-Z evolution. We find mixed evidence of faster divergence on the Z chromosome than autosomes, with significantly higher divergence being found in ancestral repeats, but not at 4- or 0-fold degenerate sites. Interestingly, some 4-fold sites appear to be selectively constrained, which may mislead analyses that use these sites as the neutral reference (e.g., dN/dS). Consistent with other studies in birds, the mutation rate is significantly higher in males than females, and the long-term Z-to-autosome effective population size ratio is only 0.5, significantly lower than the expected value of 0.75. These are indicative of male-driven evolution and high variance in male reproductive success, respectively. We find no evidence for an increased efficacy of positive selection on the Z chromosome. In contrast, the Z chromosome in great tits appears to be affected by increased genetic drift, which has led to detectable signals of weakened intensity of purifying selection. These results provide further evidence that the Z chromosome often has a low effective population size, and that this has important consequences for its evolution. They also highlight the importance of considering multiple factors that can affect the rate of evolution and effective population sizes of sex chromosomes.

Crystallographic characterization of ferritin from Sinonovacula constricta

Ferritins are ubiquitous iron-binding proteins that are mainly related to iron storage, detoxification and innate immunity. Here, we present the crystal structure of a marine invertebrate ferritin from Sinonovacula constricta at a resolution of 1.98 Å. The S. constricta ferritin (ScFer) possessed some structural similarities with vertebrate ferritins, and they shared a well-conserved architecture composed of five α-helical bundles that assembled into a cage-like structure with 24-subunits. The structure of ScFer also showed iron binding sites in the 3-fold channel, ferroxidase center, and putative nucleation sites. Further, electrostatic potential calculations suggested that the electrostatic gradient of the 3-fold channel could provide a guidance mechanism for iron entering the ferritin cavity.

First principles micro-kinetic model of catalytic non-oxidative dehydrogenation of ethane over close-packed metallic facets

Catalytic dehydrogenation of light alkanes may offer more efficient routes to selectively producing light olefins, which are some of the most important chemical building blocks in the industry, in terms of scale. We present a descriptor based micro-kinetic model of the trends in selectivity and activity of non-oxidative dehydrogenation of ethane over close-packed metal facets and through varied reaction conditions. Our model predicts and explains the experimentally observed promotion effect on turnover rate from co-feeding hydrogen as an effect of the shifting equilibria in steady state. At low conversion reaction conditions over Pt, the path to ethene goes through ethane dehydrogenation to ethyl, CH3CH2∗, then to ethene while the non-selective pathway to methane and deeply dehydrogenated species is predicted to go through dehydrogenation via CH3CH∗. This implies that the desorption step of ethene is not the limiting step for selectivity and that geometric effects that stabilize CH2CH2∗ compared to CH3CH∗ are desirable properties of a better catalyst. Removing reactive bridge and 3-fold sites facilitates this, which may be achievable by sufficient concentrations of tin in platinum. The included model code furthermore provides a base for easy tuning and for expanding the study to other thermodynamic conditions, other facets, alloys or the reaction network to longer hydrocarbons or to oxidative pathways.

A quantum-chemical study of the CO dissociation mechanism on low-index Miller planes of ϴ-Fe3C

Abstract Spin-polarized density functional theory was employed to determine the preferred CO bond dissociation mechanism on low-index Miller surfaces of ϴ-Fe3C in the context of Fischer-Tropsch synthesis. Compared to the most reactive (111) surface of bcc-Fe on which CO binds in a 7-fold coordination, CO prefers to locate in 3-fold or 4-fold sites on the carburized surfaces due to the presence of interstitial C atoms at or below the surface. An important finding is that the lowest activation energies for direct CO bond dissociation are associated with the presence of step-like sites, similar to the case of metallic surfaces. We could identify such sites for 3 out of the 9 investigated surfaces, namely the (111), 1 1 ¯ 1 , and (010) terminations of ϴ-Fe3C. On the other hand, H-assisted CO dissociation is preferred on the 0 1 ¯ 1 , (001), and (100) surfaces. The other (011), (110), and (101) surfaces are inert with CO dissociation barriers close to or exceeding the CO adsorption energy. A kinetic analysis shows that the (111) surface (direct CO dissociation) and the ( 0 1 ¯ 1 ) surface (H-assisted CO dissociation via HCO) display comparable CO bond dissociation rates, much higher than the rates computed for the other surfaces. Together these two surfaces make up ca. 28% of the surface enclosing a Wulff nanoparticle of ϴ-Fe3C. Using an atomic population analysis, we show that the activation barrier for C-O bond dissociation correlates well with the bond order of adsorbed CO. This implies that pre-activation of CO is important for lowering the overall activation barrier. The present work demonstrates that the high-temperature ϴ-Fe3C phase is highly active towards CO bond dissociation, which is the essential first step in the Fischer-Tropsch reaction. Several of the exposed surfaces present lower overall CO dissociation barriers than α-Fe (known to be unstable under Fischer-Tropsch conditions) and the χ-carbide of Fe (usually assumed to be the most stable phase of Fe-carbide under Fischer-Tropsch conditions). Notably, the activity of the (111) surface is higher than that of a stepped cobalt surface.

Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have

BackgroundAmong the four bases, guanine is the most susceptible to damage from oxidative stress. Replication of DNA containing damaged guanines results in G to T mutations. Therefore, the mutations resulting from oxidative DNA damage are generally expected to predominantly consist of G to T (and C to A when the damaged guanine is not in the reference strand) and result in decreased GC content. However, the opposite pattern was reported 16 years ago in a study of prokaryotic genomes. Although that result has been widely cited and confirmed by nine later studies with similar methods, the omission of the effect of shared ancestry requires a re-examination of the reliability of the results.ResultsWhen aerobic and obligate aerobic prokaryotes were mixed together and anaerobic and obligate anaerobic prokaryotes were mixed together, phylogenetic controlled analyses did not detect significant difference in GC content between aerobic and anaerobic prokaryotes. This result is consistent with two generally neglected studied that had accounted for the phylogenetic relationship. However, when obligate aerobic prokaryotes were compared with aerobic prokaryotes, anaerobic prokaryotes, and obligate anaerobic prokaryotes separately using phylogenetic regression analysis, a significant positive association was observed between aerobiosis and GC content, no matter it was calculated from whole genome sequences or the 4-fold degenerate sites of protein-coding genes. Obligate aerobes have significantly higher GC content than aerobes, anaerobes, and obligate anaerobes.ConclusionsThe positive association between aerobiosis and GC content could be attributed to a mutational force resulting from incorporation of damaged deoxyguanosine during DNA replication rather than oxidation of the guanine nucleotides within DNA sequences. Our results indicate a grade in the aerobiosis-associated mutational force, strong in obligate aerobes, moderate in aerobes, weak in anaerobes and obligate anaerobes.

Insights into the Mechanism of Ammonia Decomposition on Molybdenum Nitrides Based on DFT Studies

Ammonia can be used to produce carbon-free hydrogen for fuel cells and is considered as a key player in a noncarbon economy. In the present study, we investigated ammonia decomposition on Mo2N(100) and (111) surfaces using density functional theory calculations. The stepwise dissociation of ammonia over the surface Mo atom on Mo2N(100) has activation barriers >1.0 eV for all three N–H bonds. In contrast, the activation barriers for dissociating the first and second N–H bond in 3-fold Mo sites on the (111) surface are only 0.64 and 0.22 eV, respectively, whereas the activation barrier for breaking the last N–H bond is 1.12 eV. Coupling of NHx species with intrinsic surface N atoms does not always promote N–H bond activation but the formation of NlatNHx species needs to overcome a high activation barrier. Consequently, N–N coupling is not expected to have significant contributions to overall ammonia dissociation. Our results also showed that recombinative desorption of N atoms involves the formation of high...

Evidence for Strong Fixation Bias at 4-fold Degenerate Sites Across Genes in the Great Tit Genome

It is well established that GC content varies across the genome in many species and that GC biased gene conversion, one form of meiotic recombination, is likely to contribute to this heterogeneity. Bird genomes provide an extraordinary system to study the impact of GC biased gene conversion owed to their specific genomic features. They are characterised by a high karyotype conservation with substantial heterogeneity in chromosome sizes, with up to a dozen large macrochromosomes and many smaller microchromosomes common across all bird species. This heterogeneity in chromosome morphology is also reflected by other genomic features, such as smaller chromosomes being gene denser, more compact and more GC rich relative to their macrochromosomal counterparts - illustrating that the intensity of GC biased gene conversion varies across the genome. Here we study whether it is possible to infer heterogeneity in GC biased gene conversion rates across the genome using a recently published method that accounts for GC biased gene conversion when estimating branch lengths in a phylogenetic context. To infer the strength of GC biased gene conversion we contrast branch length estimates across the genome both taking and not taking non-stationary GC composition into account. Using simulations we show that this approach works well when GC fixation bias is strong and note that the number of substitutions along a branch is consistently overestimated when GC biased gene conversion is not accounted for. We use this predictable feature to infer the strength of GC dynamics across the great tit genome by applying our new test statistic to data at 4-fold degenerate sites from three bird species - great tit, zebra finch and chicken - three species that are among the best annotated bird genomes to date. We show that using a simple one-dimensional binning we fail to capture a signal of fixation bias as observed in our simulations. However, using a multidimensional binning strategy, we find evidence for heterogeneity in the strength of fixation bias, including AT fixation bias. This highlights the difficulties when combining sequence data across different regions in the genome.

Synthesis and synchrotron X-ray characterization of two 2D Hoffman related compounds [Ni(p-Xylylenediamine)nNi(CN)4] and [Ni(p-tetrafluoroxylylenediamine)nNi(CN)4

Synchrotron X-ray single crystal structure determination of two 2D Hofmann-related compounds, [Ni(p-Xylyenediamine)n-tetracyanonickelate] (abbreviated as Ni-pXdam) and [Ni(tetrafluoro-p-Xylyenediamine)n-tetracyanonickelate] (abbreviated as Ni-pXdamF4), have been conducted. Both the pXdam and pXdamF4 ligands contain two short chains of -CH2NH2 at the para-positions of a phenyl ring. These flexible chains link the 6-fold coordinated Ni2 sites throughout the network. In Ni-pXdam, the closed-2D network of [Ni-(CN-Ni1/4-)4]∞ is broken into 1D chains, leaving the C≡N groups at the trans-positions of the Ni(CN)4 moiety unbridged. The resulting 1D chains [(trans-)-NC-Ni(CN)2-CN-Ni-]∞ runs along the [010] direction of the unit cell. The pXdam ligands bridge in pair between the Ni atoms of the adjacent chains. The catenation structure of [Ni{(pXdam)}]∞ could be referred to as double -1D. In Ni-pXdamF4, the -CH2NH2 ligands connect the neighboring chains via the 6-fold Ni2 site. Surrounding the 4-fold Ni1 site, the two trans terminal C≡N groups were replaced by the Lewis base NH3 during the synthesis process, therefore preventing the propagation of the 2D net to form a 3D network. Computed pore volume of both compounds indicated that there is not sufficient space in the structure to accommodate gas molecules. In both compounds, hydrogen bonds were found, and solvent of crystallization was absent due to the limited free space in the structure.

Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions

Reconstruction of the evolution of start codons in 36 groups of closely related bacterial and archaeal genomes reveals purifying selection affecting AUG codons. The AUG starts are replaced by GUG and especially UUG significantly less frequently than expected under the neutral expectation derived from the frequencies of the respective nucleotide triplet substitutions in non-coding regions and in 4-fold degenerate sites. Thus, AUG is the optimal start codon that is actively maintained by purifying selection. However, purifying selection on start codons is significantly weaker than the selection on the same codons in coding sequences, although the switches between the codons result in conservative amino acid substitutions. The only exception is the AUG to UUG switch that is strongly selected against among start codons. Selection on start codons is most pronounced in evolutionarily conserved, highly expressed genes. Mutation of the start codon to a sub-optimal form (GUG or UUG) tends to be compensated by mutations in the Shine-Dalgarno sequence towards a stronger translation initiation signal. Together, all these findings indicate that in prokaryotes, translation start signals are subject to weak but significant selection for maximization of initiation rate and, consequently, protein production.

Semihydrogenation of Acetylene on Al5Co2 Surfaces

Density functional theory calculations are used to investigate the catalytic properties of the low-index surfaces of Al5Co2 toward the semihydrogenation of acetylene. Adsorption energies of species involved in the reaction (H, C2H2, C2H3, and C2H4) are calculated on the (001), (100), and (21̅0) surfaces. Hydrogen adsorption sites are found to be stabilized by subsurface cobalt atoms, showing an electron donor character. Scaling relations between the adsorption energies of C2Hx are established. Surface activity has been investigated on the (21̅0) surface. A possible reaction path for the semihydrogenation of acetylene is proposed using nudged elastic band calculations, starting from a 3-fold adsorption site made of three aluminum atoms. The corresponding activation energy of the rate-controlling step is calculated to be 60 kJ mol–1. The activation energy of the rate-controlling step toward total hydrogenation is evaluated to be 106 kJ mol–1, thus suggesting a selective surface for catalysis.

Variation in the Intensity of Selection on Codon Bias over Time Causes Contrasting Patterns of Base Composition Evolution in Drosophila.

Four-fold degenerate coding sites form a major component of the genome, and are often used to make inferences about selection and demography, so that understanding their evolution is important. Despite previous efforts, many questions regarding the causes of base composition changes at these sites in Drosophila remain unanswered. To shed further light on this issue, we obtained a new whole-genome polymorphism data set from D. simulans. We analyzed samples from the putatively ancestral range of D. simulans, as well as an existing polymorphism data set from an African population of D. melanogaster. By using D. yakuba as an outgroup, we found clear evidence for selection on 4-fold sites along both lineages over a substantial period, with the intensity of selection increasing with GC content. Based on an explicit model of base composition evolution, we suggest that the observed AT-biased substitution pattern in both lineages is probably due to an ancestral reduction in selection intensity, and is unlikely to be the result of an increase in mutational bias towards AT alone. By using two polymorphism-based methods for estimating selection coefficients over different timescales, we show that the selection intensity on codon usage has been rather stable in D. simulans in the recent past, but the long-term estimates in D. melanogaster are much higher than the short-term ones, indicating a continuing decline in selection intensity, to such an extent that the short-term estimates suggest that selection is only active in the most GC-rich parts of the genome. Finally, we provide evidence for complex evolutionary patterns in the putatively neutral short introns, which cannot be explained by the standard GC-biased gene conversion model. These results reveal a dynamic picture of base composition evolution.

Substoichiometric Molybdenum Sulfide Phases with Catalytically Active Basal Planes

Molybdenum sulfide (MoS2) is widely recognized for its catalytic activities where the edges of the crystals turn over reactions. Generating sulfur defects on the basal plane of MoS2 can improve its catalytic activity, but generally, there is a lack of model systems for understanding metal-centered catalysis on the basal planes. Here, we synthesized a new phase of substoichiometric molybdenum sulfide (s-MoSx) on a sulfur-enriched copper substrate. The basal plane of s-MoSx contains chemically reactive Mo-rich sites that can undergo dynamic dissociative adsorption/desorption processes with molecular hydrogen, thus demonstrating its usefulness for hydrogen-transfer catalysis. In addition, scanning tunneling microscopy was used to monitor surface-directed Ullmann coupling of 2,8-dibromo-dibenzothiophene molecules on s-MoSx nanosheets, where the 4-fold symmetric surface sites on s-MoSx direct C-C coupling to form cyclic tetramers with high selectivity.

Shape and Size of Cobalt Nanoislands Formed Spontaneously on Cobalt Terraces during Fischer-Tropsch Synthesis.

Cobalt-based catalysts undergo a massive and spontaneous reconstruction to form uniform triangular nanoislands under Fischer-Tropsch (FT) conditions. This reconstruction is driven by the unusual and synergistic adsorption of square-planar carbon and CO at the 4-fold edge sites of the nanoislands, driving the formation of triangular islands. The size of the nanoislands is determined by the balance between energy gain from creating C/CO-covered edges and energy penalty to create C/CO-covered corners. For carbon chemical potentials corresponding to FT conditions, triangular Co islands with 45 Co atoms (about 2 nm) are the most stable surface structure. Decreasing the carbon chemical potential and hence the stability of square-planar carbon favors the formation of larger islands, until reconstruction becomes unfavorable and CO-covered terraces are thermodynamically the most stable. The predicted structure of the islands is consistent with in situ scanning tunneling microscopy images obtained for the first time under realistic FT reaction conditions on a Co(0001) surface.

Comparative Genomics of Two Closely Related Wolbachia with Different Reproductive Effects on Hosts.

Wolbachia pipientis are obligate intracellular bacteria commonly found in many arthropods. They can induce various reproductive alterations in hosts, including cytoplasmic incompatibility, male-killing, feminization, and parthenogenetic development, and can provide host protection against some viruses and other pathogens. Wolbachia differ from many other primary endosymbionts in arthropods because they undergo frequent horizontal transmission between hosts and are well known for an abundance of mobile elements and relatively high recombination rates. Here, we compare the genomes of two closely related Wolbachia (with 0.57% genome-wide synonymous divergence) that differ in their reproductive effects on hosts. wVitA induces a sperm–egg incompatibility (also known as cytoplasmic incompatibility) in the parasitoid insect Nasonia vitripennis, whereas wUni causes parthenogenetic development in a different parasitoid, Muscidifurax uniraptor. Although these bacteria are closely related, the genomic comparison reveals rampant rearrangements, protein truncations (particularly in proteins predicted to be secreted), and elevated substitution rates. These changes occur predominantly in the wUni lineage, and may be due in part to adaptations by wUni to a new host environment, or its phenotypic shift to parthenogenesis induction. However, we conclude that the approximately 8-fold elevated synonymous substitution rate in wUni is due to a either an elevated mutation rate or a greater number of generations per year in wUni, which occurs in semitropical host species. We identify a set of genes whose loss or pseudogenization in the wUni lineage implicates them in the phenotypic shift from cytoplasmic incompatibility to parthenogenesis induction. Finally, comparison of these closely related strains allows us to determine the fine-scale mutation patterns in Wolbachia. Although Wolbachia are AT rich, mutation probabilities estimated from 4-fold degenerate sites are not AT biased, and predict an equilibrium AT content much less biased than observed (57–50% AT predicted vs. 76% current content at degenerate sites genome wide). The contrast suggests selection for increased AT content within Wolbachia genomes.

First principles study of nanoscale mechanism of oxygen adsorption on lanthanum zirconate surfaces

Lanthanum zirconate (La2Zr2O7) is a rare-earth pyrochlore material, which has been proposed as a promising thermal barrier coating (TBC) material due to its low thermal conductivity and high temperature phase stability. At elevated temperatures, degradation of La2Zr2O7 may occur due to adsorption of oxygen (O2) on La2Zr2O7 surfaces. This paper investigates nanoscale mechanism of O2 adsorption on La2Zr2O7 coating surfaces using the density functional theory (DFT) calculations. La2Zr2O7 surface energies on (001), (011) and (111) planes are calculated. The surface free energy of (011) plane is lower than those of (001) and (111) planes. On (001), (011) and (111) planes of La2Zr2O7, the lowest adsorption energy occurs at 4-fold site, bridge site, and 3-fold-FCC site, respectively. Among all calculated cases, the lowest adsorption energy site is 3-fold-FCC on (111) plane, which is confirmed by the Bader charge transfer analyses. Charge density difference analyses show that the 3-fold-FCC site on (111) surface has the largest charge density, suggesting the strongest interaction between O2 and La2Zr2O7 surface.

DFT simulations and microkinetic modelling of 1-pentyne hydrogenation on Cu20 model catalysts

Adsorption and dissociation of H2 and hydrogenation of 1-pentyne on neutral and anionic Cu20 clusters have been investigated using the density functional theory and microkinetic modelling. Molecular adsorption of H2 is found to occur strictly at atop sites. The H2 dimer is activated upon adsorption, and the dissociation occurs with moderate energy barriers. The dissociated H atoms reside preferentially on 3-fold face and 2-fold edge sites. Based on these results, the reaction paths leading to the partial and total hydrogenation of 1-pentyne have been studied step-by-step. The results suggest that copper clusters can display selective activity on the hydrogenation of alkyne and alkene molecules. The hydrogenated products are more stable than the corresponding initial reactants following an energetic staircase with the number of added H atoms. Stable semi-hydrogenated intermediates are formed before the partial (1-pentene) and total (pentane) hydrogenation stages of 1-pentyne. The microkinetic model analysis shows that C5H10 is the dominant product. Increasing the reactants (C5H8/H2) ratio enhances the formation of products (C5H10 and C5H12).

A computational study on the energetics and mechanisms for the dissociative adsorption of SiHx(x = 1–4) on W(1 1 1) surface

The adsorption and dissociation mechanisms of SiHx(x=1–4) species on W(111) surface have been investigated by using the periodic density functional theory with the projector-augmented wave approach. The adsorption of all the species on four surface sites: top (T), bridge (B), shallow (S), and deep (D) sites have been analyzed. For SiH4 on a top site, T-SiH4(a), it is more stable with an adsorption energy of 2.6kcal/mol. For SiH3, the 3-fold shallow site is most favorable with adsorption energy of 46.0kcal/mol. For SiH2, its adsorption on a bridge site is most stable with 73.0kcal/mol binding energy, whereas for SiH and Si the most stable adsorption configurations are on 3-fold deep sites with very high adsorption energies, 111.8 and 134.7kcal/mol, respectively. The potential energy surfaces for the dissociative adsorption of all SiHx species on the W(111) surface have been constructed using the CINEB method. The barriers for H-atom migration from SiHx(a) to its neighboring W atoms, preferentially on B-sites, were predicted to be 0.4, 1.0, 4.5 and, 8.0kcal/mol, respectively, for x=4, 3, 2, and 1, respectively. The adsorption energy of the H atom on a bridge site on the clean W(111) surface was predicted to be 65.9kcal/mol, which was found to be slightly affected by the co-adsorption of SiHx−1 within ± 1kcal/mol.