Exploring the nature of the interactions between the molecules of the sodium dodecyl sulfate and water in crystal phases and in the water/vacuum interface.

The nature of the interaction between the molecules of the sodium dodecyl sulfate surfactant forming two crystal phases, one anhydrous, NaC12H25O4S and the other, NaC12H25O4S.H2O, hydrated with one water molecule for unit cell, has been studied in detail using the quantum theory of atoms in molecules and a localized electron detector function. It was found that for the anhydrous crystal, the head groups of the surfactant molecules are linked into a head-to-head pattern, by a bond path network of Na-O ionic bonds, where each Na+ atom is attached to four S O 4 - groups. For the hydrated crystal, in addition to these four bonds for Na+, two additional ones appear with the oxygen atoms of the water molecules, forming a bond paths network of ionic Na-O bonds, that link the Na+ atoms with the S O 4 - groups and the H2O molecules. Each H2O molecule is bonded to two S O 4 - groups via hydrogen bonds, while the S O 4 - groups are linked to a maximum of four Na+ atoms. The phenomenon of aggregation of the sodium dodecyl sulfate molecules at the liquid water/vacuum interface was studied using NVT molecular dynamics simulations. We have found that for surfactant aggregates, the Na+ ions are linked to a maximum of three SO4 - groups and three water molecules that form Na-O bonds. Unlike hydrated crystal, each of the O atoms that make these Na-O bonds is linked to only one Na+ ion. Despite these differences, like the crystal phases, the surfactant molecules tend to form a head-to-head network pattern of ionic Na-O bonds that link their heads. The present results indicate that the clustering of anionic surfactant at the water/vacuum interface is a consequence of the electrostatic alignment of the cationic and anionic groups as occurs in the crystalline phases of sodium dodecyl sulfate.

Exploring the nature of the H-bonds between the human class II MHC protein, HLA-DR1 (DRB*0101) and the influenza virus hemagglutinin peptide, HA306-318, using the quantum theory of atoms in molecules.

The nature of the H-bonds between the human protein HLA-DR1 (DRB*0101) and the hemagglutinin peptide HA306-318 has been studied using the Quantum Theory of Atoms in Molecules for the first time. We have found four H-bond groups: one conventional CO··HN bond group and three nonconventional CO··HC, π··HC involving aromatic rings and HN··HCaliphatic groups. The calculated electron density at the determined H-bond critical points suggests the follow protein pocket binding trend: P1 (2,311) >> P9 (1.109) > P4 (0.950) > P6 (0.553) > P7 (0.213) which agrees and reveal the nature of experimental findings, showing that P1 produces by a long way the strongest binding of the HLA-DR1 human protein molecule with the peptide backbone as consequence of the vast number of H-bonds in the P1 area and at the same time the largest specific binding of the peptide Tyr308 residue with aromatic residues located at the binding groove floor. The present results suggest the topological analysis of the electronic density as a valuable tool that allows a non-arbitrary partition of the pockets binding energy via the calculated electron density at the determined critical points.

Exploring the electron density localization in MoS2 nanoparticles using a localized-electron detector: Unraveling the origin of the one-dimensional metallic sites on MoS2 catalysts.

The nature of the electron density localization in two MoS2 nanoclusters containing eight rows of Mo atoms, one with 100% sulphur coverage at the Mo edges (n8_100S) and the other with 50% coverage (n8_50S) was studied using a localized-electron detector function defined in the local moment representation. For n8_100S, pairs of neighboring S2 dimers cover the edges and the electron density localization function analysis shows the presence of a local triangular-shaped ring zone of highly delocalized electrons along these edges, which corresponds to a good metallic conductor zone. The optimized geometry analysis shows that the Mo-S2 bond length is much longer than that of the Mo-S bonds inside the cluster. The removal of one S atom from each sulphur dimer to create a cluster with 50% coverage produces a general compressive stress on the cluster optimized geometry, which shortens the Mo-S bond length, particularly at the edge. The electron density location function analysis shows that close to the cluster corners, a zone of highly delocalized electron zones with a characteristic semiconductor pattern and broken one-dimensional metallic ring was generated. These results suggest that the Mo-S2 bond elongation produced by the sulphur dimers is similar to a MoS2 monolayer under tensile strain and is the origin of the one-dimensional metallic sites at the Mo-edges. In general, the present findings show excellent agreement with the key features of the reported ambient pressure X-ray photoemission spectra and the corresponding simulated scanning tunneling microscopy images.

Dynamics of Surfactant Clustering at Interfaces and Its Influence on the Interfacial Tension: Atomistic Simulation of a Sodium Hexadecane-Benzene Sulfonate-Tetradecane-Water System.

The process of equilibration of the tetradecane-water interface in the presence of sodium hexadecane-benzene sulfonate is studied using intensive atomistic molecular dynamics simulations. Starting as an initial point with all of the surfactants at the interface, it is obtained that the equilibration time of the interface (several microseconds) is orders of magnitude higher than previously reported simulated times. There is strong evidence that this slow equilibration process is due to the aggregation of surfactants molecules on the interface. To determine this fact, temporal evolution of interfacial tension and interfacial formation energy are studied and their temporal variations are correlated with cluster formation. To study cluster evolution, the mean cluster size and the probability that a molecule of surfactant chosen at random is free are obtained as a function of time. Cluster size distribution is estimated, and it is observed that some of the molecules remain free, whereas the rest agglomerate. Additionally, the temporal evolution of the interfacial thickness and the structure of the surfactant molecules on the interface are studied. It is observed how this structure depends on whether the molecules agglomerate or not.

On the electron density localization in elemental cubic ceramic and FCC transition metals by means of a localized electrons detector.

The electron density localization in insulator and semiconductor elemental cubic materials with diamond structure, carbon, silicon, germanium, and tin, and good metallic conductors with face centered cubic structure such as α-Co, Ni, Cu, Rh, Pd, Ag, Ir, Pt, and Au, was studied using a localized electrons detector defined in the local moment representation. Our results clearly show an opposite pattern of the electron density localization for the cubic ceramic and transition metal materials. It was found that, for the elemental ceramic materials, the zone of low electron localization is very small and is mainly localized on the atomic basin edges. On the contrary, for the transition metals, there are low-valued localized electrons detector isocontours defining a zone of highly delocalized electrons that extends throughout the material. We have found that the best conductors are those in which the electron density at this low-value zone is the lowest.

C library for topological study of the electronic charge density.

The topological study of the electronic charge density is useful to obtain information about the kinds of bonds (ionic or covalent) and the atom charges on a molecule or crystal. For this study, it is necessary to calculate, at every space point, the electronic density and its electronic density derivatives values up to second order. In this work, a grid-based method for these calculations is described. The library, implemented for three dimensions, is based on a multidimensional Lagrange interpolation in a regular grid; by differentiating the resulting polynomial, the gradient vector, the Hessian matrix and the Laplacian formulas were obtained for every space point. More complex functions such as the Newton-Raphson method (to find the critical points, where the gradient is null) and the Cash-Karp Runge-Kutta method (used to make the gradient paths) were programmed. As in some crystals, the unit cell has angles different from 90°, the described library includes linear transformations to correct the gradient and Hessian when the grid is distorted (inclined). Functions were also developed to handle grid containing files (grd from DMol® program, CUBE from Gaussian® program and CHGCAR from VASP® program). Each one of these files contains the data for a molecular or crystal electronic property (such as charge density, spin density, electrostatic potential, and others) in a three-dimensional (3D) grid. The library can be adapted to make the topological study in any regular 3D grid by modifying the code of these functions.

Exploring the structure-solubility relationship of asphaltene models in toluene, heptane, and amphiphiles using a molecular dynamic atomistic methodology.

The solubility parameters, δ, of several asphaltene models were calculated by mean of an atomistic NPT ensemble. Continental and archipelago models were explored. A relationship between the solubility parameter and the molecule structure was determined. In general, increase of the fused-rings number forming the aromatic core and the numbers of heteroatoms such as oxygen, nitrogen, and sulfur produces an increase of the solubility parameter, while increases of the numbers and length of the aliphatic chains yield a systematic decrease of this parameter. Molecules with large total carbon atom number at the tails, n(c), and small aromatic ring number, n(r), exhibit the biggest values of δ, while molecules with small n(c) and large n(r) show the smallest δ values. A good polynomial correlation δ = 5.967(n(r)/n(c)) - 3.062(n(r)/n(c))(2) + 0.507(n(r)/n(c))(3) + 16.593 with R(2) = 0.965 was found. The solubilities of the asphaltene models in toluene, heptane, and amphiphiles were studied using the Scatchard-Hildebrand and the Hansen sphere methodologies. Generally, there is a large affinity between the archipelago model and amphiphiles containing large aliphatic tails and no aromatic rings, while continental models show high affinity for amphiphiles containing an aromatic ring and small aliphatic chains.

Stability of intermediates in the glycerol hydrogenolysis on transition metal catalysts from first principles.

The hydrogenolysis reaction catalyzed by a transition metal solid catalyst is a potential way to transform glycerol to 1,2-propylene glycol or 1,3-propylene glycol, two important chemicals. We explore the thermodynamic profile of this reaction from first principle simulation, comparing Ni, Rh and Pd catalysts modeled by (111) surfaces. The stability of adsorbed reactants, dehydrated intermediates, and hydrogenated propylene glycol is compared, with a special focus on the factors controlling the selectivity of the reaction. From a global thermodynamic view point, the formation of 1,2-propylene glycol is favored, and in addition the most stable intermediates in the gas phase (acetol and 1,2-aldol) lead to the formation of this product. The metal catalyst has three roles. First it stabilizes the dehydrated intermediates and renders the dehydration more exothermic. Second, the adsorption on the surface modifies the relative stability of the dehydrated intermediates, with implications on the reaction selectivity. Third it catalyses the hydrogenation step, leading to propylene glycol.

First-principles study of low Miller index Ni3S2 surfaces in hydrotreating conditions.

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.

Nature of the Lewis acid sites on molybdenum and ruthenium sulfides: an electrostatic potential study.

The energy of formation and the Lewis acid strength of sulfur vacancies or coordinative unsaturated sites on the MoS2 edges were studied using density functional theory for periodic systems and an electrostatic potential-based methodology. The results suggest that the more energetically favorable sites are located on the sulfur edges; however, their Lewis acid strength is considerably smaller than the site acidity at the molybdenum edges. The acid strength for the reported most hydrodesulfurization active site of RuS2 was also determined. In general, the Lewis acid for the site on RuS2 is 100% smaller than the sites on the Mo edges and around 20% larger than the most favorable site on the S edges of MoS2. Binding of the pyridine molecule in the eta1 adsorption configuration on the considered sites has corroborated the trend of Lewis acidity suggested by the electrostatic potential methodology.

Coverage effects and the nature of the metal-sulfur bond in S/Au(111): high-resolution photoemission and density-functional studies.

The bonding of sulfur to surfaces of gold is an important subject in several areas of chemistry, physics, and materials science. Synchrotron-based high-resolution photoemission and first-principles density-functional (DF) slab calculations were used to study the interaction of sulfur with a well-defined Au(111) surface and polycrystalline gold. Our experimental and theoretical results show a complex behavior for the sulfur/Au(111) interface as a function of coverage and temperature. At small sulfur coverages, the adsorption of S on fcc hollow sites of the gold substrate is energetically more favorable than adsorption on bridge or a-top sites. Under these conditions, S behaves as a weak electron acceptor but substantially reduces the density-of-states that gold exhibits near the Fermi edge. As the sulfur coverage increases, there is a weakening of the Au-S bonds (with a simultaneous reduction in the Au --> S charge transfer and a modification in the S sp hybridization) that facilitates changes in adsorption site and eventually leads to S-S bonding. At sulfur coverages above 0.4 ML, S(2) and not atomic S is the more stable species on the gold surface. Formation of S(n)(n > 2) species occurs at sulfur coverages higher than a monolayer. Very similar trends were observed for the adsorption of sulfur on polycrystalline surfaces of gold. The S atoms bonded to Au(111) display a unique mobility/reactivity not seen on surfaces of early or late transition metals.

A simple theoretical model to study the voltage dependence of the electronic structure of phenyl ethylene oligomers.

Although very few measurements have appeared in the open literature and there seems to be a controversy about the existence of the NDR phenomenon in molecules, the prospects of building such systems have attracted significant attention. In the work reported in this paper we used a model based on DFT calculations of the electronic structure of the 2'-amino-4,4'-di(ethynylphenyl)-5'-nitro-1-benzenethiolate molecule (previously reported to exhibit NDR behavior) in a capacitor-like electric field that mimics the potential spatial profile of the junction. Our results suggest that in these systems, there seems to be a correlation between a substantial charge density rearrangement of the neutral bridge at a threshold voltage and the NDR behavior observed in previous experiments. Our results highlight the importance of inclusion of the field in the study of electrified interfaces. We applied this model to a fluorine-substituted conjugated diethynylphenyl molecule and found that these calculations predict similar behavior. Results based on extended system calculations, including electrode-molecule interactions, confirm the validity of the model based on the isolated molecule and suggest the use of these simple models to rationally design molecular devices with similar switching characteristics.