Hydrazine network on Cu(111) surface: A Density Functional Theory approach

We have used first-principles calculations, including a correction for the dispersive forces (DFT-D2), to investigate the arrangement of hydrazine (N2H4) molecules upon adsorption on the Cu(111) surface, showing that surface–molecule interactions affect the process most. Our calculations provide insight into the interplay between lateral adsorbate–adsorbate and vertical adsorbate–substrate interactions. We found that the main contributors to the assembly of the hydrazine layers are the binding interactions between the adsorbates and the substrate. The dispersion forces are predominant in both vertical and lateral interactions, whereas hydrogen-bonding is least important and organisation of the N2H4 monolayers is therefore primarily due to the long-range interactions. Optimised geometries for several hydrazine conformations were found to be coverage-dependent. The electronic properties such as charge density and density of states have been calculated for different hydrazine coverages, and indicated that no charge transfer occurs between molecules. Scanning tunnelling microscopy images were simulated, where the observed protrusions arise from the trans conformers. We also found that the effect of hydrazine adsorption on the Cu(111) surface energy is negligible and further investigation of other Cu facets is needed to determine the N2H4 effect on the nanoparticles' morphology. Finally, we have simulated the temperature programmed desorption of different coverages of hydrazine from the Cu(111) resulting in desorption peaks between 150 and 200 K

Atomistic Modeling of Collagen Proteins in Their Fibrillar Environment

Molecular dynamics simulations can aid studies of the structural and physicochemical properties of proteins, by predicting their dynamics,-energetics, and interactions with their local environment at the atomistic level. We argue that nonstandard protocols are needed to realistically model collagen proteins, which in their biological state aggregate to form collagen fibrils, and so should not be treated as fully solvated molecules. A new modeling approach is presented that can account for the local environment of collagen molecules within a fibril and which therefore simulates aspects of their behavior that would not otherwise be distinguished. This modeling approach exploits periodic boundaries to replicate the supermolecular arrangement of collagen proteins within the fibril, in an approach. that is more commonly associated with modeling crystalline solids rather than mesoscopic protein aggregates. Initial simulations show agreement with experimental observations and corroborate. theories of the fibril's structure

Selective hydrogenation of CO on Fe3S4{111}: a computational study

Fischer–Tropsch (FT) synthesis has been a recursive method to form valuable molecules from syngas. Metal surfaces have been extensively studied as FT catalysts; among them, iron presents several phases under reaction conditions, oxides and carbides, as active sites for the FT and reverse water gas shift reaction. We present CO reduction on an iron sulfide phase with spinel structure, Fe3S4, also considering the pathways where C–O dissociates leaving CHx species on the surface, which may feed longer aliphatic chains via the FT process. We analysed the thermodynamic and kinetic availability of each step leading to O and OH species co-adsorbed on the surface as well as the formation of H2O from the hydrogenation of the alcohol group in the molecule. This detailed analysis led to energy profiles on both active sites of the surface, and we conclude that this Fe3S4 surface is highly selective towards the formation of methanol, in full agreement with experimental results. These findings point out that the C–C bond formation on greigite takes place through a hydroxycarbene FT mechanism

Towards a morphology of cobalt nanoparticles: size and strain effects

Cobalt nanoparticles with diameters of 8 nm have recently shown promising performance for biomedical applications. However, it is still unclear how the shape of cobalt clusters changes with size when reaching the nanoparticle range. In the present work, density functional theory calculations have been employed to compare the stabilities of two non-crystalline (icosahedron and decahedron) shapes, and three crystalline motifs (hcp, fcc, and bcc) for magic numbered cobalt clusters with up to 1500 atoms, based on the changes in the cohesive energies, coordination numbers, and nearest-neighbour distances arising from varying geometries. Obtained trends were extrapolated to a 104 size range, and an icosahedral shape was predicted for clusters up to 5500 atoms. Larger sized clusters adopt hcp stacking, in correspondence with the bulk phase. To explain the crystalline/non-crystalline crossovers, the contributions of the elastic strain density and twin boundary from the specimen surfaces to the cohesive energy of different motifs were evaluated. These results are expected to aid the design and synthesis of cobalt nanoparticles for applications ranging from catalysis to biomedical treatments

Adsorption and Desulfurization Mechanism of Thiophene on Layered FeS(001), (011), and (111) Surfaces: A Dispersion-Corrected Density Functional Theory Study

Layered transition-metal chalcogenides have emerged as a fascinating new class of materials for catalysis. Here, we present periodic density functional theory (DFT) calculations of the adsorption of thiophene and the direct desulfurization reaction pathways on the (001), (011), and (111) surfaces of layered FeS. The fundamental aspects of the thiophene adsorption, including the initial adsorption geometries, adsorption energies, structural parameters, and electronic properties, are presented. From the calculated adsorption energies, we show that the flat adsorption geometries, wherein the thiophene molecule forms multiple π-bonds with the FeS surfaces, are energetically more favorable than the upright adsorption geometries, with the strength of adsorption decreasing in the order FeS(111) > FeS(011) > FeS(001). The adsorption of the thiophene onto the reactive (011) and (111) surfaces is shown to be characterized by charge transfer from the interacting Fe d-band to the π-system of the thiophene molecule, which causes changes of the intramolecular structure including loss of aromaticity and elongation of the C–S bonds. The thermodynamic and kinetic analysis of the elementary steps involved in the direct desulfurization of thiophene on the reactive FeS surfaces is also presented. Direct desulfurization of thiophene occurs preferentially on the (111) surface, as reflected by the overall exothermic reaction energy calculated for the process (ER = −0.15 eV), with an activation energy of 1.58 eV

A density functional theory study of the hydrogenation and reduction of the thio-spinel Fe3S4{111} surface

The mineral greigite, Fe3S4, shows promising electro-reduction activity, especially towards carbon dioxide conversion to small organic molecules. We have employed density functional theory calculations with correction for the long-range dispersion forces to investigate the behavior of hydrogen on the greigite{111} surface. We have studied the adsorption, diffusion, surface reduction and associative (i.e. Volmer–Tafel mechanism) and molecular desorption of hydrogen as a function of its coverage. We found that (i) the H ad-atoms adsorb on S sites far from metallic centres in the topmost surface layer; (ii) the reduction of greigite by hydrogen is energetically unfavorable at any surface coverage; and (iii) molecular hydrogen evolution has a transition state at ∼0.5 eV above the energy of the reactants on Fe3S4{111}, which is very similar to the barrier found experimentally on Pt{111}. We have also determined the electrode potential under room conditions at which the H2 evolution reaction becomes energetically barrierless

Effect of strontium inclusion on the bioactivity of phosphate-based glasses

We have conducted first-principles and classical molecular dynamics simulations of various compositions of strontium-containing phosphate glasses, to understand how strontium incorporation will change the glasses’ activity when implanted into the body (bioactivity). To perform the classical simulations, we have developed a new interatomic potential, which takes account of the polarizability of the oxygen ions. The Sr–O bond length is ∼2.44–2.49 Å, and the coordination number is 7.5–7.8. The Qn distribution and network connectivity were roughly constant for these compositions. Sr bonds to a similar number of phosphate chains as Ca does; based on our previous work (Christie et al. in J Phys Chem B 117:10652, 2013), this implies that SrO ↔ CaO substitution will barely change the dissolution rate of these glasses and that the bioactivity will remain essentially constant. Strontium could therefore be incorporated into phosphate glass for biomedical applications

A kinetic model of water adsorption, clustering and dissociation on the Fe3S4{001} surface

The interaction of water with catalyst surfaces is a common process which requires investigation. Here, we have employed density functional theory calculations to investigate the adsorption of up to ten water molecules on the {001} surface of greigite (Fe3S4), which owing to its redox properties, is of increasing interest as a catalyst, e.g. in electro-catalysis. We have systematically analyzed and characterized the modes of water adsorption on the surface, where we have considered both molecular and dissociative adsorption processes. The calculations show that molecular adsorption is the predominant state on these surfaces, from both a thermodynamic and kinetic point of view. We have explored the molecular dispersion on the surface under different coverages and found that the orientation of the molecule, and therefore the surface dipole, depends on the number of adsorbed molecules. The interactions between the water molecules become stronger with an increasing number of water molecules, following an exponential decay which tends to the interaction energy found in bulk water. We have also shown the evolution of the infra-red signals as a function of water coverage relating to the H-bond networks formed on the surface. Next we have included these results in a classical micro-kinetic model, which introduced the effects of temperature in the simulations, thus helping us to derive the water cluster size on the greigite surface as a function of the initial conditions of pressure, temperature and external potential. The kinetic model concluded that water molecules agglomerate in clusters instead of wetting the surface, which agrees with the low hydrophilicity of Fe3S4. Clusters consisting of four water molecules was shown to be the most stable cluster under a wide range of temperatures and external potential

Mechanistic insights into the Cu(I) oxide-catalyzed conversion of CO2 to fuels and chemicals: A DFT approach

Periodic, self-consistent, density functional theory calculations with corrections via a Hubbard U parameter, and inclusion of dispersive forces (DFT-D2), have been employed to study CO2 activation and conversion on the Cu2O (1 1 1) surface. CO2 hydrogenation on the Cu2O (1 1 1) surface was investigated systematically, and the respective microscopic reaction mechanisms were elucidated. We show that, whereas CO2 dissociation is not energetically allowed on the Cu2O (1 1 1) surface, CO2 hydrogenation to a formate intermediate is more favourable than the formation of a carboxyl intermediate. Further hydrogenation from formate to formic acid is energetically allowed, where formate combines with strongly adsorbed surface hydrogen to form bidentate formic acid moieties. Formation of both the formate and the formic acid from adsorbed CO2 and surface hydrogen are exothermic reactions

Mechanisms of CO2 Capture in Ionic Liquids: A Computational Perspective

We present computational studies of CO2 sorption in two different classes of ionic liquid. The addition of carbon dioxide to four superbase ionic liquids, [P3333][Benzim], [P3333][124Triz], [P3333][123Triz] and [P3333][Bentriz] was studied using DFT approach and considering anions alone and individual ion pairs. Addition of CO2 to the anion alone clearly resulted in the formation of a covalently-bound carbamate function with the strength of binding correlated to experimental capacity. In the ion pair however the cation significantly alters the nature of the bonding such that the overall cohesive energy is reduced. Formation of a strong carbamate function occurs at the expense of weakening the interaction between anion and cation. In [N111][L-ALA], a representative amino acid ionic liquid, evidence was found for a low-enegy monomolecular mechanism for carbamate formation, explaining the 1:1 molar uptake ratio observed in some amino acid ionic liquids. The mechanism involves proton transfer to to the carboxylate group of the aminate anion