An understanding of chemoselective hydrogenation on crotonaldehyde over Pt(111) in the free energy landscape: The microkinetics study based on first-principles calculations

Microkinetic model is developed in the free energy landscape based on density functional theory (DFT) to quantitatively investigate the reaction mechanism of chemoselective partial hydrogenation of crotonaldehyde to crotyl alcohol over Pt(1 1 1) at the temperature of 353 K. Three different methods (mobile, immobile and collision theory models) were carried out to obtain free energy barrier of adsorption/desorption processes. The results from mobile and collision theory models are similar. The calculated TOFs from both models are close to the experiment value. However, for the immobile model, in which the free energy barrier of desorption approaches the energy barrier, the calculated TOF is 2 orders of magnitude lower than the other models. The difficulty of adsorption/ desorption may be overestimated in the immobile model. In addition, detailed analyses show that for the surface hydrogenation elementary steps, the entropy and internal energy effects are small under the reaction condition, while the zero-point-energy (ZPE) correction is significant, especially for the multi-step hydrogenation reaction. The total energy with the ZPE correction approaches to the full free energy calculation for the surface reaction under the reaction condition. (c) 2011 Elsevier B.V. All rights reserved.

Reaction Mechanisms of Crotonaldehyde Hydrogenation on Pt(111): Density Functional Theory and Microkinetic Modeling

The microkinetics based on density function theory (DFT) calculations is utilized to investigate the reaction mechanism of crotonaldehyde hydrogenation on Pt(111) in the free energy landscape. The dominant reaction channel of each hydrogenation product is identified. Each of them begins with the first surface hydrogenation of the carbonyl oxygen of crotonaldehyde on the surface. A new mechanism, 1,4-addition mechanism generating enols (butenol), which readily tautomerize to saturated aldehydes (butanal), is identified as a primary mechanism to yield saturated aldehydes instead of the 3,4-addition via direct hydrogenation of the ethylenic bond. The calculation results also show that the full hydrogenation product, butylalcohol, mainly stems from the deep hydrogenation of surface open-shell dihydrogenation intermediates. It is found that the apparent barriers of the dominant pathways to yield three final products are similar on P(111), which makes it difficult to achieve a high selectivity to the desired crotyl alcohol (COL).

Activity and coke formation of nickel and nickel carbide in dry reforming: A deactivation scheme from density functional theory

Dry reforming is a promising reaction to utilise the greenhouse gases CO2 and CH4. Nickel-based catalysts are the most popular catalysts for the reaction, and the coke formation on the catalysts is the main obstacle to the commercialisation of dry reforming. In this study, the whole reaction network of dry reformation on both flat and stepped nickel catalysts (Ni(111) and Ni(211)) as well as nickel carbide (flat: Ni3C(001); stepped: Ni3C(111)) is investigated using density functional theory calculations. The overall reaction energy profiles in the free energy landscape are obtained, and kinetic analyses are utilised to evaluate the activity of the four surfaces. By careful examination of our results, we find the following regarding the activity: (i) flat surfaces are more active than stepped surfaces for the dry reforming and (ii) metallic nickel catalysts are more active than those of nickel carbide, and therefore, the phase transformation from nickel to nickel carbide will reduce the activity. With respect to the coke formation, the following is found: (i) the coke formation probability can be measured by the rate ratio of CH oxidation pathway to C oxidation pathway (r(CH)/r(C)) and the barrier of CO dissociation, (ii) on Ni(111), the coke is unlikely to form, and (iii) the coke formations on the stepped surfaces of both nickel and nickel carbide can readily occur. A deactivation scheme, using which experimental results can be rationalised, is proposed. 

Population-based local search for protein folding simulation in the MJ energy model and cubic lattices

We present experimental results on benchmark problems in 3D cubic lattice structures with the Miyazawa-Jernigan energy function for two local search procedures that utilise the pull-move set: (i) population-based local search (PLS) that traverses the energy landscape with greedy steps towards (potential) local minima followed by upward steps up to a certain level of the objective function; (ii) simulated annealing with a logarithmic cooling schedule (LSA). The parameter settings for PLS are derived from short LSA-runs executed in pre-processing and the procedure utilises tabu lists generated for each member of the population. In terms of the total number of energy function evaluations both methods perform equally well, however. PLS has the potential of being parallelised with an expected speed-up in the region of the population size. Furthermore, both methods require a significant smaller number of function evaluations when compared to Monte Carlo simulations with kink-jump moves. (C) 2009 Elsevier Ltd. All rights reserved.

Probing the Unfolded Configurations of a β-Hairpin Using Sketch-Map

This work examines the conformational ensemble involved in β-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent molecules is used, and this complex energy landscape is sampled by means of parallel tempering metadynamics simulations. The ensemble of configurations explored is analyzed using the recently proposed sketch-map algorithm. Further simulations allow us to probe how mutations affect the structures adopted by this protein. We find that many of the configurations adopted by a mutant are the same as those adopted by the wild-type protein. Furthermore, certain mutations destabilize secondary-structure-containing configurations by preventing the formation of hydrogen bonds or by promoting the formation of new intramolecular contacts. Our analysis demonstrates that machine-learning techniques can be used to study the energy landscapes of complex molecules and that the visualizations that are generated in this way provide a natural basis for examining how the stabilities of particular configurations of the molecule are affected by factors such as temperature or structural mutations.

Stochastic protein folding simulation in the three-dimensional HP-model

We present results from three-dimensional protein folding simulations in the HP-model on ten benchmark problems. The simulations are executed by a simulated annealing-based algorithm with a time-dependent cooling schedule. The neighbourhood relation is determined by the pull-move set. The results provide experimental evidence that the maximum depth D of local minima of the underlying energy landscape can be upper bounded by D < n(2/3). The local search procedure employs the stopping criterion (In/delta)(D/gamma) where m is an estimation of the average number of neighbouring conformations, gamma relates to the mean of non-zero differences of the objective function for neighbouring conformations, and 1-delta is the confidence that a minimum conformation has been found. The bound complies with the results obtained for the ten benchmark problems. (c) 2008 Elsevier Ltd. All rights reserved.

Influence of the anion on the electrical conductivity and glass formation of 1-butyl-3-methylimidazolium ionic liquids

Six ionic liquids based on the 1-butyl-3-methylimidazolium cation have been studied. As anions Cl-, Br-, I-, [NCS](-), [N(CN)(2)](-), and [BF4](-) were selected. The electrical conductivities were determined between 173 and 393 K based on impedance measurements in the frequency range from 0.1 to 10(7) Hz. The electrical conductivity increases, whereas the glass transition temperature, the fragility, and the low temperature activation energy decrease with increasing anion size. The results can be understood from the changing anion-cation interaction strength with changing anion size and from the energy landscape interpretation of the glass transition dynamics. (C) 2010 American Institute of Physics. [doi:10.1063/1.3455892]

Numerical assessment of potential impacts of hydraulically fractured Bowland Shale on overlying aquifers

Natural gas extracted from hydraulically fractured shale formations potentially has a big impact on the global energy landscape. However, there are concerns of potential environmental impacts of hydraulic fracturing of the shale formations, particularly those related to water quality. To evaluate the potential impact of hydraulically fractured shale on overlying aquifers, we conduct realizations of numerical modeling simulations to assess fluid flow and chloride transport from a synthetic Bowland Shale over a period of 11,000 years. The synthetic fractured shale was represented by a three-dimensional discrete fracture model that was developed by using the data from a Bowland Shale gas exploration in Lancashire, UK. Chloride mass exchange between fractures and the rock matrix was fully accounted for in the model. The assessment was carried out to investigate fluid and chloride mass fluxes before, during, and after hydraulic fracturing of the Bowland Shale. Impacts of the upward fracture height and aperture, as well as hydraulic conductivity of the multilayered bedrock system, are also included this assessment. This modeling revealed that the hydraulically fractured Bowland Shale is unlikely to pose a risk to its overlying groundwater quality when the induced fracture aperture is ≤200 µm. With the fracture aperture ≥1000 µm, the upward chloride flux becomes very sensitive to the upward fracture height growth and hydraulic conductivity of the multilayered bedrock system. In the extremely unlikely event of the upward fracture growth directly connecting the shale formation to the overlying Sherwood Sandstone aquifer with the fracture aperture ≥1000 µm, the upward chloride mass flux could potentially pose risks to the overlying aquifer in 100 years. The model study also revealed that the upward mass flux is significantly intercepted by the horizontal mass flux within a high permeable layer between the Bowland Shale and its overlying aquifers, reducing further upward flux toward the overlying aquifers.

Electrical conductivity and glass formation in nitrile-functionalized pyrrolidinium bis(trifluoromethylsulfonyl)imide ionic liquids: chain length and odd–even effects of the alkyl spacer between the pyrrolidinium ring and the nitrile group

The electrical conductivity of a series of pyrrolidinium bis(trifluoromethylsulfonyl)imide ionic liquids, functionalized with a nitrile (cyano) group at the end of an alkyl chain attached to the cation, was studied in the temperature range between 173 K and 393 K. The glass formation of the ionic liquids is influenced by the length of the alkyl spacer separating the nitrile function from the pyrrolidinium ring. The electrical conductivity and the viscosity do not show a monotonic dependence on the alkyl spacer length, but rather an odd-even effect. An explanation for this behavior is given, including the potential energy landscape picture for the glass transition.

Theory of the near K-edge structure in electron energy loss spectroscopy

Arguments are given that lead to a formalism for calculating near K-edge structure in electron energy loss spectroscopy (EELS). This is essentially a one electron picture, while many body effects may be introduced at different levels, such as the local density approximation to density functional theory or the GW approximation to the electron self-energy. Calculations are made within the all electron LMTO scheme in crystals with complex atomic and electronic structures, and these are compared with experiment. (c) 2004 Elsevier B.V. All rights reserved.

The machinist landscape:Land Art Generator Initiative (Competition)

THE MACHINIST LANDSCAPE: AN ENTROPIC GRID OF VARIANCE
‘By drawing a diagram, a ground plan of a house, a street plan to the location of a site, or a topographic map, one draws a “logical two dimensional picture”. A “logical picture” differs from a natural or realistic picture in that it rarely looks like the thing it stands for.’
A Provisional Theory of Non-Sites, Robert Smithson (1968)

Between design and ground there are variances, deviations and gaps. These exist as physical interstices between what is conceptualised and what is realised; and they reveal moments in the design process that resist the reconciliation of people and their environment (McHarg 1963). The Machinist Landscape interrogates the significance of these variances through the contrasting processes of coppice and photovoltaic energy. It builds on the potential of these gaps, and in doing so proposes that these spaces of variance can reveal the complexity of relationships between consumption and remediation, design and nature.
Fresh Kills Park, and in particular the draft master plan (2006), offers a framework to explore this artificial construct. Central to the Machinist Landscape is the analysis of the landfill gas collection system, planned on a notional 200ft grid. Variations are revealed between this diagrammatic grid measure and that which has been constructed on the site. These variances between the abstract and the real offer the Machinist Landscape a powerful space of enquiry. Are these gaps a result of unexpected conditions below ground, topographic nuances or natural phenomena? Does this space of difference, between what is planned and what is constructed, have the potential to redefine the dynamic processes and relations with the land?
The Machinist Landscape is structured through this space of variance with an ‘entropic grid’, the under-storey of which hosts a carefully managed system of short-rotation coppice (SRC). The coppice, a medieval practice related to energy, product, and space, operates on theoretical and programmatic levels. It is planted along a structure of linear bunds, stabilized through coppice pole retaining structures and enriched with nutrients from coppice produced bio-char. Above the coppice is built an upper-storey of photovoltaic (PV); its structures fabricated from the coppiced timber and the PV produced with graphene from coppice charcoal processes.

An Energy Descriptor To Quantify Methane Selectivity in Fischer-Tropsch Synthesis:A Density Functional Theory Study

Selectivity is a fundamental issue in heterogeneous catalysis. In this study, the CH(4) selectivity in Fischer-Tropsch synthesis is chosen to be investigated: CH4 selectivity on Rh, Co, Ru, Fe, and Re surfaces is computed by first-principles methods. In conjunction with kinetic analyses, we are able to derive the effective barrier difference between methane formation and chain growth (Delta E(eff)) to quantify the CH(4) selectivity. By using this energy descriptor, the ranking of methane selectivity predicted from density functional theory (DFT) calculations is consistent with experimental work. Moreover, a linear correlation between Delta E(eff) and the chemisorption energy of C + 4H (Delta H) is found. This fundamental finding possesses the following significance: (i) it shows that the selectivity, which appears to have kinetic characteristics, is largely determined by thermodynamic properties; and (ii) it suggests that an increase of the binding strength of C + 4H will suppress methane selectivity.