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This paper describes the characterization of structural, energetic, and electric properties of the molecular complexes between Orinoco belt resins through the application of computational molecular mechanics (MM), semi-empirical parametrization (PM6), and density functional theory (DFT) (PW91 and HCTH) in conjunction with the double numeric and polarized (DNP) basis set. The resin sources for the studied molecules are Orinoco belt vacuum residues (Carabobo, Hamaca, Merey, Merey-Mesa, and Zuata). Molecular structures of these compounds were proposed from analysis of experimental characterization. The study of molecular interactions has shown that these resins are able to form stable van der Waals complexes, where their computed stability has a large dependence upon the applied theory level. A qualitative description of the formation of these complexes could be obtained with these methodologies. In particular, MM overestimates resin interaction energies when compared to PM6 and DFT (PW91 and HCTH) results. ...

The nature of small nickel sulfide clusters was explored using the atoms in molecules theory and a based-electrostatic potential methodology. It was found that Ni$_{3}$S$_{4}$, whose structure corresponds to a C$_{3V}$ {7, 9, 3} pyramid, should be (at 0 K) the most stable of the studied nickel sulfide clusters. Electrostatic potential results suggest that the Lewis acidity of the studied cluster is much larger (and therefore much more HDS reactive) than the respective acidity of the practically inactive Ni$_{3}$S$_{2}$ (111) surfaces. Atomistic thermodynamic calculations have shown that at typical HDS working conditions very small particles of non supported nickel sulphide should be mainly present as Ni$_{3}$S$_{4}$ cluster.

MoS$_{2}$ bulk packing was studied using the Atoms in Molecules Theory. The network of bond paths describing the atomic connectivity has shown that the crystal graph of this material results from the packing of three types of polyhedra containing cage critical points localized at d, f and a Wyckoff position. Alternatively, the crystal packing can be described by means of the basin of the Mo and S atoms with $D_{3h}$ and $C_{3v}$ symmetry, respectively. These basins display the full local point-group symmetry at the nuclear sites, and fill the space without overlapping. S-S secondary bonds in the interlayer region of this layered material were also determined. The presence of these bonds is fundamental for the found packing of the MoS$_{2}$ bulk.

Density functional theory (DFT) calculations combined with surface thermodynamic arguments and the Gibbs-Curie-Wulff equilibrium morphology formalism have been employed to explore the effect of the reaction conditions, temperature (T), and gas-phase partial pressures (p h2 and p h2s ) on the stability of low Miller index ruthenium sulfide (RuS 2 ) surfaces. The calculated thermodynamic surface stabilities and the resulting equilibrium morphology models suggest that unsupported RuS 2 nanoparticles in HDS conditions are like to a polyhedron with six, eight, and twelve (100), (111), and (102) faces, respectively. The area of these faces covers about 40%, 37%, and 23% of the total particle, respectively. The atomic basins of the outermost individual atoms of the exposed surfaces were determined using the quantum theory of atoms in molecules methodology. Direct visualization of these basins has shown that a hole just at the middle of the outermost sulfur basins provides access to uncovered metal sites. Analysis of the electrostatic potential mapped onto a selected electron density isocontour (0.001 au) on the exposed surface reveals a very high potential reactivity of these holes toward electrodonating reagents. Consequently, the high attraction between these uncovered sites and S atoms coming from reagent polluting molecules makes these kinds of particles quite active for HDS catalysis.

The nature of the MoS 2 catalyst edge was studied using the atoms in molecules theory. The network of bond paths describing the atomic connectivity has shown that the exposed graph of this edge results from the packing of polyhedra, with six vertexes and four faces, located at the Mo edges and polyhedra, with five vertexes and three faces, located at both sides of the S edge. The former polyhedra are bonded by a much bigger electron density suggesting a relationship between this fact and the smaller necessary energy to create a sulfur vacancy on the S edges than the Mo edges. Additionally, we have found that potential active sites on the catalyst surface can be localized visualizing the outermost interatomic surfaces.

The nature of the interaction of water molecules with the surface of a set of experimentally well-studied alkane−amidethiols adsorbed on a gold(111) surface and its effect on the water contact angle have been studied by carrying out a systematic determination of the topology of electrostatic potential using ab initio density functional theory methods for periodic systems. The obtained results have shown that the water contact angle decreases systematically as the number of minima by surface cell unit and the electrostatic potential magnitude at these minima, and consequently the adsorption strength, increases. Thus, this electrostatic potential magnitude can be used as a measure of the efficiency and ability of a chemical group for wetting of a surface by water.

Binding between water and models of poly(ethylene oxide), (CH2−CH2−O)n, n = 2−40, has been studied using the topographic features of the electrostatic potential, V(r), and standard density functional theory methods. It was found that, in general, the contour around the minima of the oxygen atoms overlap forming a negative-valued spiral coiled around a positive-valued helix. The positive zone defines a helical groove in the O−C−C−O units where minima lone pairs critical points are located. Topological analysis of the water molecule has also suggested that the attractive electrostatic effect between the positive water O−H zone and the negative PEO lone pairs plays an important role in the hydrogen bonding of the PEO−water system. Thus, the V(r) topology predicts a coil of water molecules around the PEO chain forming hydrogen bonding with two sites of ether oxygens. This coil is formed in such a way that more water molecules accumulate on the cavities surrounding the poly(ethylene oxide)'s oxygen atoms where...

In this work, the topology of the electrostatic potential using density functional theory for periodic systems was used to study the nature of the interaction of water with laponite surfaces; an uncharged sheet model was also used. The topological analysis predicts that for uncharged surfaces the adsorption mode is such that the water molecules are adsorbed almost parallel to the surface. For laponite surfaces, where there is a net charge, the adsorption mode involves electrostatic repulsion between the negative lone pairs on the water molecules and the ones on the surface oxygen atoms. As a consequence, the water molecules bind to the surface in a perpendicular and tilted approach, minimizing the repulsive interactions. The advantage of using the topology of the electrostatic potential as an efficient method to describe the electrostatic interactions between adsorbates and surfaces is also discussed.

The “atoms in molecules” theory (AIM) is very useful to extract significant information from the electronic density, ρ( r ) . In the present paper, we show the implementation in WIEN 97 of some algorithms to determine the main elements of this novel theory (critical points of ρ( r ) , bond paths, crystal graphs, interatomic surfaces, atomic basins and atomic properties). WIEN 97 program is one successful implementation of the full-potential linearized augmented-plane wave method (FPLAPW), which allows most accurate calculations of the electronic density of crystals and surfaces using density functional theory. In order to illustrate those algorithms, they were applied to Pt and PtS bulk as two selected examples.

The interaction of a CO molecule with the (100) surface of the fcc d-block transition metals is analyzed by the topology of the Laplacian of the electronic charge density −∇ 2 ρ . This analysis shows that the atomic graph for the top atoms is an octahedron that exposes, outside the (100) surface, a vertex V top with a local maximum of charge, and four faces F top with a local minimum. The corresponding graph for the second-layer atoms is also an octahedron that exhibits a vertex V sec outside the surface. Atomic graphs for the CO molecule show that the carbon atom has a non-bonded vertex C nb , and a torus C torus of charge depletion perpendicular to the CO bond direction. Laplacian topology predicts CO perpendicular orientation in bridge- or top-sites. The bridge-site involves attractive interactions with two atoms of the surface: face (metal top atom)–vertex (C atom)–face (metal top atom). The top-site involves the attractive interaction vertex (C atom)–face (metal top atom). Attractive interaction between the surface and only one atom of the CO molecule rules out dissociation and predicts molecular adsorption.

A numerical method to analyze the topology of the electronic density regardless of how it was obtained (analytically or numerically) was implemented for the Extreme 94 program. The method allows th...

A numerical method that analyzes the topology of the Laplacian of the electronic density regardless of how it was obtained (analytically, numerically, or even experimentally) was implemented for the BUBBLE program. The method allows the study of a complex system where the electronic correlation is important, by density functional theory regardless the kind of basis set used, and allows the analysis of the Laplacian of the resulting charge density with the topological theory of Bader. The method was applied to CO and NO molecules and the Cu13, Cu45, and Fe21 clusters modeling the (100) Cu and (001) Fe surfaces, respectively.

The virial field V(r) is defined by the local statement of the quantum mechanical virial theorem, as the trace of the Schrodinger stress tensor. This field defines the electronic potential energy density of an electron at r and integrates to minus twice the electronic kinetic energy. It is the most short-ranged description possible of the local electronic potential energy and it exhibits the same transferable behavior over bounded regions of real space (corresponding to the functional groups of chemistry) as does ρ(r). This article establishes a structural homeomorphism between −V(r) and ρ(r), showing that the two fields are homeomorphic over all of the nuclear configuration space. The stable or unstable structure defined by the gradient vector field Δρ(r; X) for any configuration X of the nuclei can be placed in a one-to-one correspondence with a structure defined by the field −ΔV(r; X′). In particular, a molecular graph for ρ(r) defining a molecular structure is mirrored by a corresponding virial graph for V(r) and the lines of maximum density linking bonded nuclei in the former field are matched by a set of lines of maximally negative potential energy density in the latter. The homeomorphism is also geometrically faithful, an equilibrium geometry in general, exhibiting equivalent structures in the two fields. The demonstration that the virial field, whose integrated value equals twice the total energy, is essentially just a locally scaled version of the electron density is suggestive of possible new approaches in density functional theory. © 1996 John Wiley & Sons, Inc.

Density functional theory (DFT) calculations combined with surface thermodynamic arguments and the Gibbs-Curie-Wulff equilibrium morphology formalism have been employed to explore the effect of the reaction conditions, temperature (T), and gas-phase partial pressures (PH2 and PH2S) on the stability of nickel sulfide (Ni3S2) surfaces. Furthermore, the strength and nature of chemical bonds for selected Ni3S2 surface cuts were investigated with the quantum theory of atoms in molecules methodology. A particular analysis of the electrostatic potential within this theoretical framework is performed to study the potential activity of nickel sulfide nanoparticles as hydrodesulfurization (HDS) catalysts. The calculated thermodynamic surface stabilities and the resulting equilibrium morphology model suggest that unsupported Ni3S2 nanoparticles mainly expose (111) and (111) type surface faces in HDS conditions. Analysis of the electrostatic potential mapped onto a selected electron density isocontour (0.001 au) on those expose surface reveals a poor potential reactivity toward electron-donating reagents (i.e., low Lewis acidity). Consequently, a very low attraction between coordinatively unsaturated active sites (Lewis sites) exposed at the catalytic particles and the S atoms coming from reagent polluting molecules does inactive these kinds of particles for HDS.

The interaction of a CO molecule with the Fe(100) surface is analyzed by the topology of the Laplacian of the electronic charge density −∇2ρ. This analysis shows that the atomic graph of the top atoms of the Fe(100) surface is a cube that exposes a face, Ftop, with a “hole” of charge or (3,+1) critical point of −∇2ρ, whereas the corresponding graph for the second layer atoms is an octahedron that exhibits a vertex, Vsec, protruding above the Fe(100) surface, with a “peak” of charge or (3,−3) critical point of −∇2ρ. Atomic graphs determined for the CO molecule show that the carbon atom has a non-bonded vertex, CVnb, and a torus, Ctorus, of charge depletion perpendicular to the C–O bond direction. As the CO molecule approaches the surface, electron transfer towards the tilted CO in turn induces two non-bonded critical points, OVnb, on the O atom. In accordance with experimental and theoretical results, the topological theory of the Laplacian suggests that the preferred pathway for CO dissociation corresponds to the tilted orientation on the surface, in which the attractive interaction Ctorus–Vsec is enhanced by the interaction of the two OVnb with the Ftop on two Fe top atoms of the (100) surface.

Molecular orbital ab initio Hartree–Fock, post-Hartree–Fock at the MP2 and QCISD levels, and density functional theory calculations of the dipole moment, the topology of the electronic density, ρ(r), and its Laplacian, [Formula: see text], for CO and NO molecules are reported. The results obtained confirm that density functional methods provide remarkably good electronic properties and a good description of the topology of ρ(r) and [Formula: see text]. The Becke exchange functional with the correlation functional of Lee, Yang, and Parr was used to calculate the electronic density of the (100) Cu surface. Topological analysis of ρ(r) shows that the crystal graph corresponds to square pyramids between the atoms of the top of the surface and the atoms of the second layer The topological analysis of [Formula: see text] shows that the atomic graph of the Cu surface exhibits one (3,−3) local charge concentration surrounded by four (3,+1) local charge depletion points. Additionally, there is a (3,+3) local depletion in the midpoint between each of four contiguous Cu atoms corresponding to the active site for the adsorption of the (3,−3) local charge concentration on the C atom of the CO or the N atom of the NO molecule. The larger value of the [Formula: see text] at the nonbonded charge concentration on the atoms and the geometrical configuration of these critical points favor the interaction of the NO over the CO molecule with the (100) Cu surface. This result is in accord with the known reaction barriers for these molecules. Key words: density functional theory, Laplacian of the electronic density, (100) Cu surface, carbon monoxide, nitrogen monoxide, molecular graph, atomic graph.