Hydrodesulfurization of Dibenzothiophene: A Machine Learning Approach.

The hydrodesulfurization (HDS) process is widely used in the industry to eliminate sulfur compounds from fuels. However, removing dibenzothiophene (DBT) and its derivatives is a challenge. Here, the key aspects that affect the efficiency of catalysts in the HDS of DBT were investigated using machine learning (ML) algorithms. The conversion of DBT and selectivity was estimated by applying Lasso, Ridge, and Random Forest regression techniques. For the estimation of conversion of DBT, Random Forest and Lasso offer adequate predictions. At the same time, regularized regressions have similar outcomes, which are suitable for selectivity estimations. According to the regression coefficient, the structural parameters are essential predictors for selectivity, highlighting the pore size, and slab length. These properties can connect with aspects like the availability of active sites. The insights gained through ML techniques about the HDS catalysts agree with the interpretations of previous experimental reports.

Electronic structure behavior of PbO2, IrO2, and SnO2 metal oxide surfaces (110) with dissociatively adsorbed water molecules as a function of the chemical potential.

A detailed analysis of the electronic structure of three different electrochemical interfaces as a function of the chemical potential (µ) is performed using the grand canonical density functional theory in the joint density functional theory formulation. Changes in the average number of electrons and the density of states are also described. The evaluation of the global softness, which measures the tendency of the system to gain or lose electrons, is straightforward under this formalism. The observed behavior of these quantities depends on the electronic nature of the electrochemical interfaces.

Establishing the Relationship between Quantum Capacitance and Softness of N-Doped Graphene/Electrolyte Interfaces within the Density Functional Theory Grand Canonical Kohn-Sham Formalism.

The joint density functional theory (JDFT) is applied in the context of the grand canonical Kohn-Sham theory to calculate the global and local softness of pristine and N-substituted graphene structures. A comparison is established between the different theoretical approaches to evaluate total capacitance, revealing that the JDFT approach presents the closest result of this property with experimental data. A model of series capacitors is used to determine the quantum and nonquantum contributions of total capacitance, which enables us to determine the limitations of the rigid band approximation for the studied systems. It is found that global chemical softness is proportional to the total capacitance measured in the experiments, when the geometry relaxation is neglected. In this context, it is possible to obtain quantum and total capacitance (and consequently softness) from an average number of electrons vs applied potential plots and the model of series capacitors. Likewise, the relation of capacitance and softness gives rise to a new definition of local capacitance within the JDFT formalism. The evaluation of global and local softness paves the way to analyze electrochemical surface reactivity as a function of applied potential for a solid-electrolyte interface.

Using local softness to reveal oxygen participation in redox processes in cathode materials.

In this paper, the use of chemical local softness s(r) is proposed as an alternative way of analyzing the initial redox processes that occur in cathode materials used for lithium-ion batteries. It is shown that the chemical local softness is a quantity able to capture the same effects as the standard analysis based on the projected density of states. Because of its own nature, the local softness reveals the atomic sites involved in charge-transfer events and allows a quantitative comparative analysis between different materials. As pointed out by Johannes et al. (Solid State Ion 286:83-89, 2016), this analysis can be used as an indicator of stability of cathode materials for Li-ion batteries.

Hydrogen bonds in methane-water clusters.

Characterization of hydrogen bonds in CH4-(H2O)12 clusters was carried out by using several quantum chemistry tools. An initial stochastic search provided around 2 500 000 candidate structures, then, using a convex-hull polygon criterion followed by gradient based optimization under the Kohn-Sham scheme, a total of 54 well defined local minima were located in the Potential Energy Surface. These structures were further analyzed through second-order many-body perturbation theory with an extended basis set at the MP2/6-311++G(d,p) level. Our analysis of Gibbs energies at several temperatures clearly suggests a structural preference toward compact water clusters interacting with the external methane molecule, instead of the more commonly known clathrate-like structures. This study shows that CH4-(H2O)12 clusters may be detected at temperatures up to 179 K, this finding provides strong support to a recently postulated hypothesis that suggests that methane-water clusters could be present in Mars at these conditions. Interestingly, we found that water to water hydrogen bonding is strengthened in the mixed clusters when compared to the isolated water dimer, which in turn leads to a weakening of the methane to water hydrogen bonding when compared to the CH4-(H2O) dimer. Finally, our evidence places a stern warning about the abilities of popular geometrical criteria to determine the existence of hydrogen bonds.

Sensing polarization effects through the analysis of the effective C6 dispersion coefficients in NaCl solutions.

Density functional theory based ab initio molecular dynamics is used to obtain microscopic details of the interactions in sodium chloride solutions. By following the changes in the atomic C6 coefficients under the Tkatchenko-Scheffler's scheme, we were able to identify two different coordination situations for the Cl(-) ion with significant different capabilities to perform dispersion interactions. This capability is enhanced when the ion-ion distance corresponds to the contact ion-pair situation. Also, the oxygen and hydrogen atoms of the water molecules change their aptitudes to interact through van der Waals like terms when they are close to the cation region of the ion-pair. These results have interesting implications on the design of force fields to model electrolyte solutions.

Grid-based algorithm to search critical points, in the electron density, accelerated by graphics processing units.

Using a grid-based method to search the critical points in electron density, we show how to accelerate such a method with graphics processing units (GPUs). When the GPU implementation is contrasted with that used on central processing units (CPUs), we found a large difference between the time elapsed by both implementations: the smallest time is observed when GPUs are used. We tested two GPUs, one related with video games and other used for high-performance computing (HPC). By the side of the CPUs, two processors were tested, one used in common personal computers and other used for HPC, both of last generation. Although our parallel algorithm scales quite well on CPUs, the same implementation on GPUs runs around 10× faster than 16 CPUs, with any of the tested GPUs and CPUs. We have found what one GPU dedicated for video games can be used without any problem for our application, delivering a remarkable performance, in fact; this GPU competes against one HPC GPU, in particular when single-precision is used.

Electronic stress as a guiding force for chemical bonding.

In the electron-preceding picture of chemical change, the paramount problem is identifying favorable changes in electronic structure. The electronic stress tensor provides this information; its eigenvectors represent electronic normal modes, pointing the way towards energetically favorable (or unfavorable) chemical rearrangements. The resulting method is well founded in both density functional theory and the quantum theory of atoms in molecules (QTAIM). Stress tensor analysis is a natural way to extend the QTAIM to address chemical reactivity. The definition and basic properties of the electronic stress tensor are reviewed and the inherent ambiguity of the stress tensor is discussed. Extending previous work in which the stress tensor was used to analyze hydrogen-bonding patterns, this work focuses on chemical bonding patterns in organic reactions. Other related material (charge-shift bonding, links to the second-density-derivative tensor) is summarized and reviewed. The stress tensor provides a multifaceted characterization of bonding and can be used to predict and describe bond formation and migration.

Pointing the way to the products? Comparison of the stress tensor and the second-derivative tensor of the electron density.

The eigenvectors of the electronic stress tensor can be used to identify where new bond paths form in a chemical reaction. In cases where the eigenvectors of the stress tensor are not available, the gradient-expansion-approximation suggests using the eigenvalues of the second derivative tensor of the electron density instead; this approximation can be made quantitatively accurate by scaling and shifting the second-derivative tensor, but it has a weaker physical basis and less predictive power for chemical reactivity than the stress tensor. These tools provide an extension of the quantum theory of atoms and molecules from the characterization of molecular electronic structure to the prediction of chemical reactivity.

Photoelectron and computational studies of the copper-nucleoside anionic complexes, Cu(-)(cytidine) and Cu(-)(uridine).

The copper-nucleoside anions, Cu(-)(cytidine) and Cu(-)(uridine), have been generated in the gas phase and studied by both experimental (anion photoelectron spectroscopy) and theoretical (density functional calculations) methods. The photoelectron spectra of both systems are dominated by single, intense, and relatively narrow peaks. These peaks are centered at 2.63 and 2.71 eV for Cu(-)(cytidine) and Cu(-)(uridine), respectively. According to our calculations, Cu(-)(cytidine) and Cu(-)(uridine) species with these peak center [vertical detachment energy (VDE)] values correspond to structures in which copper atomic anions are bound to the sugar portions of their corresponding nucleosides largely through electrostatic interactions; the observed species are anion-molecule complexes. The combination of experiment and theory also reveal the presence of a slightly higher energy, anion-molecule complex isomer in the case of the Cu(-)(cytidine). Furthermore, our calculations found that chemically bond isomers of these species are much more stable than their anion-molecule complex counterparts, but since their calculated VDE values are larger than the photon energy used in these experiments, they were not observed.

Synthesis and characterization of a coupled binuclear Cu(I)/Cu(III) complex.

The synthesis through reaction of a C(alpha),C(ortho) dilithiated phosphazene with CuBr and structural characterization of the first example of a binuclear mixed valence [Cu(I)(N(2))/Cu(III)(C(4))] complex showing a metal-metal bond, as well as its applications in cyclopropanation and oxidation reactions, are described.

Bonding and magnetism of Fe(6)-(C(6)H(6))(m), m = 1, 2.

The interactions of one and two benzene molecules with the superparamagnetic Fe(6) cluster were studied by means of gradient-corrected density functional theory. The ground state, GS, of bare Fe(6) presents a distorted octahedral structure with 2S = 20; S is the total spin. For the calculated 2S = 16 GS of the neutral Fe(6)-C(6)H(6) complex, as well as in the positive and negative ions both with 2S = 15, the benzene unit is adsorbed on one axial Fe(a) atom. The 2S = 14 GS for Fe(6)-(C(6)H(6))(2) resembles a sandwich structure, with the metal Fe(6) cluster separating the benzene rings that are bonded symmetrically on the two axial sites of Fe(6). The binding is accounted for by electrostatic interactions and by 3d-pi bonds, as revealed by the molecular orbitals. Though each C-Fe bond is weak, eta(6) coordinations were indicated by the topology of the electronic density. The 3d-pi bonding is reflected by the adiabatic ionization energies and electron affinities, which are smaller than those of bare Fe(6). The computed IR spectra show vibrational bands near those of bare benzene; some forbidden IR modes in benzene and in Fe(6) become IR active in Fe(6)-(C(6)H(6))(1,2). The results show a strong perturbation of the electronic structure of Fe(6). The decrease of its magnetic moment implies that the magnetic effects play an important role in the adsorption of benzene.

Electron binding energies and Dyson orbitals of Al5Om- (m=3,4,5) and Al5O5H2-.

Photoelectron spectra of Al(5)O(m)(-) (m=3-5) and of the anion produced by the dissociative adsorption of a water molecule by Al(5)O(4)(-) are interpreted with density-functional geometry optimizations and electron-propagator calculations of vertical electron detachment energies. For Al(5)O(3)(-), Al(5)O(4)(-), and Al(5)O(5)H(2)(-), the observed signals may be attributed to the most stable isomer of each anion. For Al(5)O(5)(-), the features in the photoelectron spectrum are due to three almost isoenergetic isomers.

Sequential addition of H2O, CH3OH, and NH3 to Al3O3-: a theoretical study.

Photoelectron spectra of two species, Al3O3(H2O)2- and Al3O3(CH3OH)2-, that are produced by the addition of two water or methanol molecules to Al3O3- are interpreted with density-functional geometry optimizations and electron propagator calculations of vertical electron detachment energies. In both cases, there is only one isomer that is responsible for the observed spectral features. A high barrier to the addition of a second molecule may impede the formation of Al3O3N2H6- clusters in an analogous experiment with NH3.

Metal-Molecule Interactions To Produce Hydrogen: What Do They Have in Common?

The main purpose of this work is to study metal-molecule interactions that can lead to the production of molecular hydrogen. Two systems were chosen for this analysis: yttrium atom and clusters interacting with the simple electron donor ammonia (NH3) and copper atoms and ions with imidazole. For yttrium with ammonia as well as for copper with imidazole there is a charge-transfer process from the metal to the molecule that promotes the dissociation of the hydrogen atoms.

Are structures with Al-H bonds represented in the photoelectron spectrum of Al3O4H2-?

Photoelectron spectra of Al3O4H2- clusters formed by reactions of Al3O3- with water molecules have been interpreted recently in terms of dissociative absorption products with hydroxide and oxide anions that are coordinated to aluminum cations. Alternative isomers with Al-H bonds have lower energies, but barriers to hydrogen migrations that break O-H bonds and create Al-H bonds are high. Ab initio electron propagator calculations of the vertical electron detachment energies of the anions indicate that the species with hydrides cannot be assigned to the chief features in the photoelectron spectrum. Therefore, the previously studied dissociative absorption products are the structures that are most likely to be probed in the photoelectron spectra.

Addition of water, methanol, and ammonia to Al3O3- clusters: reaction products, transition states, and electron detachment energies.

Products of reactions between the book and kite isomers of Al3O3- and three important molecules are studied with electronic structure calculations. Dissociative adsorption of H2O or CH3OH is highly exothermic and proton-transfer barriers between anion-molecule complexes and the products of these reactions are low. For NH3, the reaction energies are less exothermic and the corresponding barriers are higher. Depending on experimental conditions, Al3O3- (NH3) coordination complexes or products of dissociative adsorption may be prepared. Vertical electron detachment energies of stable anions are predicted with ab initio electron propagator calculations and are in close agreement with experiments on Al3O3- and its products with H2O and CH3OH. Changes in the localization properties of two Al-centered Dyson orbitals account for the differences between the photoelectron spectra of Al3O3- and those of the product anions.

Cluster size selectivity in the product distribution of ethene dehydrogenation on niobium clusters.

Ethene reactions with niobium atoms and clusters containing up to 25 constituent atoms have been studied in a fast-flow metal cluster reactor. The clusters react with ethene at about the gas-kinetic collision rate, indicating a barrierless association process as the cluster removal step. Exceptions are Nb8 and Nb10, for which a significantly diminished rate is observed, reflecting some cluster size selectivity. Analysis of the experimental primary product masses indicates dehydrogenation of ethene for all clusters save Nb10, yielding either Nb(n)C2H2 or Nb(n)C2. Over the range Nb-Nb6, the extent of dehydrogenation increases with cluster size, then decreases for larger clusters. For many clusters, secondary and tertiary product masses are also observed, showing varying degrees of dehydrogenation corresponding to net addition of C2H4, C2H2, or C2. With Nb atoms and several small clusters, formal addition of at least six ethene molecules is observed, suggesting a polymerization process may be active. Kinetic analysis of the Nb atom and several Nb(n) cluster reactions with ethene shows that the process is consistent with sequential addition of ethene units at rates corresponding approximately to the gas-kinetic collision frequency for several consecutive reacting ethene molecules. Some variation in the rate of ethene pick up is found, which likely reflects small energy barriers or steric constraints associated with individual mechanistic steps. Density functional calculations of structures of Nb clusters up to Nb(6), and the reaction products Nb(n)C2H2 and Nb(n)C2 (n = 1...6) are presented. Investigation of the thermochemistry for the dehydrogenation of ethene to form molecular hydrogen, for the Nb atom and clusters up to Nb6, demonstrates that the exergonicity of the formation of Nb(n)C2 species increases with cluster size over this range, which supports the proposal that the extent of dehydrogenation is determined primarily by thermodynamic constraints. Analysis of the structural variations present in the cluster species studied shows an increase in C-H bond lengths with cluster size that closely correlates with the increased thermodynamic drive to full dehydrogenation. This correlation strongly suggests that all steps in the reaction are barrierless, and that weakening of the C-H bonds is directly reflected in the thermodynamics of the overall dehydrogenation process. It is also demonstrated that reaction exergonicity in the initial partial dehydrogenation step must be carried through as excess internal energy into the second dehydrogenation step.