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.

Magnetic structure of UO2and NpO2by first-principle methods

The magnetic structure of the actinide dioxides (AnO₂) remains a field of intense research. A noncollinear relativistic computational study of the AnO₂(An = U, Np) magnetic structure has been completed.

Liquid phase hydrogenation of CO2 to formate using palladium and ruthenium nanoparticles supported on molybdenum carbide

We report the development of palladium nanoparticles supported on Mo₂C as an active catalyst for the liquid-phase hydrogenation of CO₂ to formate under mild reaction conditions (100 °C and 2.0 MPa of a 1 : 1 CO₂ : H₂ mixture).

Molecular behaviour of phenol in zeolite Beta catalysts as a function of acid site presence: a quasielastic neutron scattering and molecular dynamics simulation study

The dynamic behaviour of phenol in zeolite Beta is strongly influenced by the presence of Brønsted acid sites.

Carbon dioxide and water co-adsorption on the low-index surfaces of TiC, VC, ZrC and NbC: a DFT study

We present a theoretical DFT study into the activation of CO₂ and H₂O by four low-index surfaces of TiC, VC, ZrC and NbC. Two distinct chemisorption pathways are found for CO₂ activation, whilst multiple surface mediated interactions between H₂O and CO₂ are reported.

Mixing thermodynamics and electronic structure of the Pt1−xNix (0 ≤ x ≤ 1) bimetallic alloy

Density functional theory simulations complemented by force-field based calculations show that the bimetallic Pt_0.5Ni_0.5 equilibrium composition is highly ordered at room conditions.

Ab initio investigation of O2 adsorption on Ca-doped LaMnO3 cathodes in solid oxide fuel cells

We present a Hubbard-corrected density functional theory (DFT+U) study of the adsorption and reduction reactions of oxygen on the pure and 25% Ca-doped LaMnO3 (LCM25) {100} and {110} surfaces. The effect of oxygen vacancies on the adsorption characteristics and energetics has also been investigated. Our results show that the O2 adsorption/reduction process occurs through the formation of superoxide and peroxide intermediates, with the Mn sites found to be generally more active than the La sites. The LCM25{110} surface is found to be more efficient for O2 reduction than the LCM25{100} surface due to its stronger adsorption of O2, with the superoxide and peroxide intermediates shown to be energetically more favorable at the Mn sites than at the Ca sites. Moreover, oxygen vacancy defect sites on both the {100} and {110} surfaces are shown to be more efficient for O2 reduction, as reflected in the higher adsorption energies calculated on the defective surfaces compared to the perfect surfaces. We show from Löwdin population analysis that the O2 adsorption on the pure and 25% Ca-doped LaMnO3 surfaces is characterized by charge transfer from the interacting surface species into the adsorbed oxygen πg orbital, which results in weakening of the O-O bonds and its subsequent reduction. The elongated O-O bonds were confirmed via vibrational frequency analysis.

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 CH_x 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.

Insight into the Nature of Iron Sulfide Surfaces During the Electrochemical Hydrogen Evolution and CO2 Reduction Reactions

Greigite and other iron sulfides are potential, cheap, earth-abundant electrocatalysts for the hydrogen evolution reaction (HER), yet little is known about the underlying surface chemistry. Structural and chemical changes to a greigite (Fe₃S₄)-modified electrode were determined at -0.6 V versus standard hydrogen electrode (SHE) at pH 7, under conditions of the HER. In situ X-ray absorption spectroscopy was employed at the Fe K-edge to show that iron-sulfur linkages were replaced by iron-oxygen units under these conditions. The resulting material was determined as 60% greigite and 40% iron hydroxide (goethite) with a proposed core-shell structure. A large increase in pH at the electrode surface (to pH 12) is caused by the generation of OH^- as a product of the HER. Under these conditions, iron sulfide materials are thermodynamically unstable with respect to the hydroxide. In situ infrared spectroscopy of the solution near the electrode interface confirmed changes in the phosphate ion speciation consistent with a change in pH from 7 to 12 when -0.6 V versus SHE is applied. Saturation of the solution with CO₂ resulted in the inhibition of the hydroxide formation, potentially due to surface adsorption of HCO₃^-. This study shows that the true nature of the greigite electrode under conditions of the HER is a core-shell greigite-hydroxide material and emphasizes the importance of in situ investigation of the catalyst under operation to develop true and accurate mechanistic models.

Calcium Phosphate Deposition on Planar and Stepped (101) Surfaces of Anatase TiO2: Introducing an Interatomic Potential for the TiO2/Ca-PO4/Water Interface

Titanium is commonly employed in orthopaedic and dental surgery, owing to its good mechanical properties. The titanium metal is usually passivated by a thin layer of its oxide, and in order to promote its integration with the biological tissue, it is covered by a bioactive material such as calcium phosphate (CaP). Here, we have investigated the deposition of calcium and phosphate species on the anatase phase of titanium dioxide (TiO₂) using interatomic potential-based molecular dynamics simulations. We have combined different force fields developed for CaP, TiO₂, and water, benchmarking the results against density functional theory calculations. On the basis of our study, we consider that the new parameters can be used successfully to study the nucleation of CaP on realistic anatase and rutile TiO₂ nanoparticles, including surface defects.

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 the DFT approach and considering anions alone and individual ion pairs. The 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 [N₁₁₁₁][l-ALA], a representative amino acid ionic liquid, evidence was found for a low-energy 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 the carboxylate group of the aminate anion.

Density functional theory characterization of the structures of H3AsO3 and H3AsO4 adsorption complexes on ferrihydrite

Reactions occurring at ferric oxyhydroxide surfaces play an important role in controlling arsenic bioavailability and mobility in natural aqueous systems. However, the mechanism by which arsenite and arsenate complex with ferrihydrite (Fh) surfaces is not fully understood and although there is clear evidence for inner sphere complexation, the nature of the surface complexes is uncertain. In this work, we have used periodic density functional theory calculations to predict the relative energies, geometries and properties of arsenous acid (H3AsO3) and arsenic acid (H3AsO4), the most prevalent form of As(iii) and As(v), respectively, adsorbed on Fh(110) surface at intermediate and high pH conditions. Bidentate binuclear (BB(Fe-O)) corner-sharing complexes are shown to be energetically favoured over monodentate mononuclear complexes (MM(Fe-O)) for both arsenic species. The inclusion of solvation effects by introducing water molecules explicitly near the adsorbing H3AsO3 and H3AsO4 species was found to increase their stability on the Fh surface. The adsorption process is shown to be characterized by hybridization between the interacting surface Fe-d states and the O and As p-states of the adsorbates. Vibrational frequency assignments of the As-O and O-H stretching modes of the adsorbed arsenic species are also presented.

Relative orientation of collagen molecules within a fibril: a homology model for homo sapiens type I collagen

Type I collagen is an essential extracellular protein that plays an important structural role in tissues that require high tensile strength. However, owing to the molecule's size, to date no experimental structural data are available for the Homo sapiens species. Therefore, there is a real need to develop a reliable homology model and a method to study the packing of the collagen molecules within the fibril. Through the use of the homology model and implementation of a novel simulation technique, we have ascertained the orientations of the collagen molecules within a fibril, which is currently below the resolution limit of experimental techniques. The longitudinal orientation of collagen molecules within a fibril has a significant effect on the mechanical and biological properties of the fibril, owing to the different amino acid side chains available at the interface between the molecules.

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.

CO2 activation and dissociation on the low miller index surfaces of pure and Ni-coated iron metal: a DFT study

We have used spin polarized density functional theory calculations to perform extensive mechanistic studies of CO₂ dissociation into CO and O on the clean Fe(100), (110) and (111) surfaces and on the same surfaces coated by a monolayer of nickel. CO₂ chemisorbs on all three bare facets and binds more strongly to the stepped (111) surface than on the open flat (100) and close-packed (110) surfaces, with adsorption energies of -88.7 kJ mol^-1, -70.8 kJ mol^-1 and -116.8 kJ mol^-1 on the (100), (110) and (111) facets, respectively. Compared to the bare Fe surfaces, we found weaker binding of the CO₂ molecules on the Ni-deposited surfaces, where the adsorption energies are calculated at +47.2 kJ mol^-1, -29.5 kJ mol^-1 and -65.0 kJ mol^-1 on the Ni-deposited (100), (110) and (111) facets respectively. We have also investigated the thermodynamics and activation energies for CO₂ dissociation into CO and O on the bare and Ni-deposited surfaces. Generally, we found that the dissociative adsorption states are thermodynamically preferred over molecular adsorption, with the dissociation most favoured thermodynamically on the close-packed (110) facet. The trends in activation energy barriers were observed to follow that of the trends in surface work functions; consequently, the increased surface work functions observed on the Ni-deposited surfaces resulted in increased dissociation barriers and vice versa. These results suggest that measures to lower the surface work function will kinetically promote the dissociation of CO₂ into CO and O, although the instability of the activated CO₂ on the Ni-covered surfaces will probably result in CO₂ desorption from the nickel-doped iron surfaces, as is also seen on the Fe(110) surface.

Reactivity of CO2 on the surfaces of magnetite (Fe3O4), greigite (Fe3S4) and mackinawite (FeS)

The growing environmental, industrial and commercial interests in understanding the processes of carbon dioxide (CO2) capture and conversion have led us to simulate, by means of density functional theory calculations, the application of different iron oxide and sulfide minerals to capture, activate and catalytically dissociate this molecule. We have chosen the {001} and {111} surfaces of the spinel-structured magnetite (Fe3O4) and its isostructural sulfide counterpart greigite (Fe3S4), which are both materials with the Fe cations in the 2+/3+ mixed valence state, as well as mackinawite (tetragonal FeS), in which all iron ions are in the ferrous oxidation state. This selection of iron-bearing compounds provides us with understanding of the effect of the composition, stoichiometry, structure and oxidation state on the catalytic activation of CO2 The largest adsorption energies are released for the interaction with the Fe3O4 surfaces, which also corresponds to the biggest conformational changes of the CO2 molecule. Our results suggest that the Fe3S4 surfaces are unable to activate the CO2 molecule, while a major charge transfer takes place on FeS{111}, effectively activating the CO2 molecule. The thermodynamic and kinetic profiles for the catalytic dissociation of CO2 into CO and O show that this process is feasible only on the FeS{111} surface. The findings reported here show that these minerals show promise for future CO2 capture and conversion technologies, ensuring a sustainable future for society.This article is part of a discussion meeting issue 'Providing sustainable catalytic solutions for a rapidly changing world'.

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.

Bulk and surface properties of metal carbides: implications for catalysis

We present a comprehensive study of the bulk and surface properties of transition metal carbides with rock salt structures and discuss their formation energies, electronic structure and potential catalytic activity.

Modelling water diffusion in plasticizers: development and optimization of a force field for 2,4-dinitroethylbenzene and 2,4,6-trinitroethylbenzene

A classical all-atom force field has been developed for 2,4,6-trinitroethylbenzene and 2,4-dinitroethylbenzene and applied in molecular dynamics simulations of the two pure and two mixed plasticizer systems. Bonding parameters and partial charges were derived through electronic and geometry optimization of the single molecules. The other required parameters were derived from values already available in the literature for generic nitro aromatic compounds, which were adjusted to reproduce to a high level of accuracy the densities of 2,4-dinitroethylbenzene, 2,4,6-trinitroethylbenzene and the energetic plasticizers K10 and R8002. This force field has been applied to both K10 and R8002, which when used as plasticizers form an energetic binder with nitrocellulose. Nitrocellulose decomposes in storage, under varying conditions, but in particular where it may become increasingly dry. Following the derivation of the force field, we have therefore applied it to calculate water diffusion coefficients for each of the different materials at 298 K and 338 K, thereby providing a starting point for understanding water behaviour in a nitrocellulose binder.

A classical all-atom force field has been developed for the plasticizer molecules 2,4,6-trinitroethylbenzene and 2,4-dinitroethylbenzene which can be used to investigate properties and energetic output of nitrocellulose-based propellants and binders.

Hidden magnetic order in plutonium dioxide nuclear fuel

The magnetic structure of PuO₂ has been investigated by computational methods. A hereto unknown longitudinal 3k AFM ground-state that retains Fm3̄m crystal symmetry has been identified.

Stability and mobility of supported Nin (n = 1–10) clusters on ZrO2(111) and YSZ(111) surfaces: a density functional theory study

We have used spin polarized density functional theory (DFT) to evaluate the geometrical resilience of Ni clusters on ZrO₂(111) and YSZ(111).

A molecular dynamics study of plasticiser migration in nitrocellulose binders

The assessment of plasticiser migration in nitrocellulose binder systems using diffusion coefficients and activation energies of diffusion.

CO2 interaction with violarite (FeNi2S4) surfaces: a dispersion-corrected DFT study

The interaction between the CO₂ molecule and the violarite FeNi₂S₄{001} and {111} surfaces is studied using different exchange–correlation functionals and long-range dispersion correction approximations.

ForceGen: atomic covalent bond value derivation for Gromacs

A large number of crystallographic protein structures include ligands, small molecules and post-translational modifications. Atomic bond force values for computational atomistic models of post-translational or non-standard amino acids, metal binding active sites, small molecules and drug molecules are not readily available in most simulation software packages. We present ForceGen, a Java tool that extracts the bond stretch and bond angle force values and equilibrium values from the Hessian of a Gaussian vibrational frequency analysis. The parameters are compatible with force fields derived using the second order tensor of the Hessian. The output is formatted with the Gromacs topology in mind. This study further demonstrates the use of ForceGen over the quantum mechanically derived structures of a small organic solvent, a naturally occurring protein crosslink derived from two amino acids following post-translational modification and the amino acid ligands of a zinc ion. We then derive Laplacian bond orders to understand how the resulting force values relate back to the quantum mechanical model. The parameterisation of the organic solvent, toluene, was verified using Molecular Mechanics simulations. The structural data from the simulation compared well with the quantum mechanical structure and the system density compared well with experimental values.

Periodic modeling of zeolite Ti-LTA

We have proposed a combination of density functional theory calculations and interatomic potential-based simulations to study the structural, electronic, and mechanical properties of pure-silica zeolite Linde Type A (LTA), as well as two titanium-doped compositions. The energetics of the titanium distribution within the zeolite framework suggest that the inclusion of a second titanium atom with configurations Ti-(Si)₀-Ti, Ti-(Si)₁-Ti, and Ti-(Si)₂-Ti is more energetically favorable than the mono-substitution. Infra-red spectra have been simulated for the pure-silica LTA, the single titanium substitution, and the configurations Ti-(Si)₀-Ti and Ti-(Si)₂-Ti, comparing against experimental benchmarks where available. The energetics of the direct dissociation of water on these Lewis acid sites indicate that this process is only favored when two titanium atoms form a two-membered ring (2MR) sharing two hydroxy groups, Ti-(OH)₂-Ti, which suggests that the presence of water may tune the distribution of titanium atoms within the framework of zeolite LTA. The electronic analysis indicates charge transfer from H₂O to the Lewis acid site and hybridization of their electronic states.