1. The mechanism of chemisorption of hydrogen atom on graphene: insights from the reaction force and reaction electronic flux.

    Journal of Chemical Physics 141(13):134701 (2014) PMID 25296822

    At the PBE-D3/cc-pVDZ level of theory, the hydrogen chemisorption on graphene was analyzed using the reaction force and reaction electronic flux (REF) theories in combination with electron population analysis. It was found that chemisorption energy barrier is mainly dominated by structural work ...
  2. Polarizability of neutral copper clusters.

    Journal of Molecular Modeling 20(9):2410 (2014) PMID 25149439

    Neutral copper clusters are characterized through their molecular structures, binding energy and electric dipole polarizability. It is shown that the mean and anisotropy of polarizability tensor are useful properties in the characterization and rationalization of reactivity and growth patterns i...
  3. The mechanism of Menshutkin reaction in gas and solvent phases from the perspective of reaction electronic flux.

    Journal of Molecular Modeling 20(9):2353 (2014) PMID 25135065

    The mechanism of Menshutkin reaction, NH(3) + CH(3)Cl = [CH(3)-NH(3)]+ + Cl-, has been thoroughly studied in both gas and solvent (H(2)O and cyclohexane) phase. It has been found that solvents favor the reaction, both thermodynamically and kinetically. The electronic activity that drives the mec...
  4. Using the reaction force and the reaction electronic flux on the proton transfer of formamide derived systems.

    Physical Chemistry Chemical Physics 16(28):14489 (2014) PMID 24618654

    In this work, we present a theoretical study of the mechanism of double proton transfer in formamide, formamide-thioformamide and thioformamide dimers. The reaction mechanisms were analyzed in terms of the energy profile and novel concepts such as the reaction force profile and reaction electron...
  5. In pursuit of negative Fukui functions: molecules with very small band gaps.

    Journal of Molecular Modeling 20(3):2162 (2014) PMID 24573501

    A justification for the likely presence of negative Fukui functions in molecules with small band gaps is given, and a computational study performed to check whether molecules with small band gaps have negative Fukui functions to a chemically significant extent is reported. While regions with neg...
  6. Electronic stress as a guiding force for chemical bonding.

    Topics in Current Chemistry 351:103 (2014) PMID 21796514

    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 u...
  7. Electronic stress as a guiding force for chemical bonding.

    Topics in Current Chemistry 351:103 (2014) PMID 21796514

    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 u...
  8. Modeling the mechanism of glycosylation reactions between ethanol, 1,2-ethanediol and methoxymethanol.

    Physical Chemistry Chemical Physics 15(33):14026 (2013) PMID 23860569

    The mechanism of the S(N)2 model glycosylation reaction between ethanol, 1,2-ethanediol and methoxymethanol has been studied theoretically at the B3LYP/6-311+G(d,p) computational level. Three different types of reactions have been explored: (i) the exchange of hydroxyl groups between these model...
  9. Is hyper-hardness more chemically relevant than expected?

    Journal of Molecular Modeling 19(7):2893 (2013) PMID 23475291

    In this work, the third derivative of the energy with respect to the number of electrons, the so-called hyper-hardness, is investigated to assess whether this quantity has a chemical meaning. To achieve this goal a new working expression for hyper-hardness is developed and analyzed. It transpire...
  10. Summer talks in Santiago III--the Politzer Conference.

    Journal of Molecular Modeling 19(7):2687 (2013) PMID 23743608

  11. In pursuit of negative Fukui functions: examples where the highest occupied molecular orbital fails to dominate the chemical reactivity.

    Journal of Molecular Modeling 19(7):2779 (2013) PMID 23090502

    In our quest to explore molecules with chemically significant regions where the Fukui function is negative, we explored reactions where the frontier orbital that indicates the sites for electrophilic attack is not the highest occupied molecular orbital. The highest occupied molecular orbital (HO...
  12. Fine structure in the transition region: reaction force analyses of water-assisted proton transfers.

    Journal of Molecular Modeling 19(7):2689 (2013) PMID 22733272

    We have analyzed the variation of the reaction force F(ξ) and the reaction force constant κ(ξ) along the intrinsic reaction coordinates ξ of the water-assisted proton transfer reactions of HX-N = Y (X,Y = O,S). The profile of the force constant of the vibration associated with the reactive mode,...
  13. Influence of the monoclinic and tetragonal zirconia phases on the water gas shift reaction. A theoretical study.

    Journal of Molecular Modeling 19(7):2885 (2013) PMID 23377895

    We present a theoretical study of the water gas shift reaction taking place on zirconia surfaces modeled by monoclinic and tetragonal clusters. In order to understand the charge transfer between the active species, in this work we analyze the influence of the geometry of monoclinic and tetragona...
  14. XXXVII Congreso de Químicos Teóricos de Expresión Latina, Quitel 2011.

    Journal of Molecular Modeling 19(5):1943 (2013) PMID 23564288

  15. A detailed look at the reaction mechanisms of substituted carbenes with water.

    Journal of Physical Chemistry A: Molecules, Spe... 117(9):1991 (2013) PMID 23398173

    Two competitive reaction mechanisms for the gas-phase chemical transformation of singlet chlorocarbene into chloromethanol in the presence of one and two water molecules are examined in detail. An analysis of bond orders and bond order derivatives as well as of properties of bond critical points...
  16. How does Pin1 catalyze the cis-trans prolyl peptide bond isomerization? A QM/MM and mean reaction force study.

    Journal of Physical Chemistry B 116(43):12972 (2012) PMID 23030417

    Pin1 represents an enzyme that specifically catalyzes the isomerization of peptide bonds between phosphorylated threonine or serine residues and proline. Despite its relevance as molecular timer in a number of biological processes related to cancer and Alzheimer disease, a detailed understanding...
  17. Insights into the mechanism of an S(N)2 reaction from the reaction force and the reaction electronic flux.

    Journal of Physical Chemistry A: Molecules, Spe... 116(40):10015 (2012) PMID 22974407

    The mechanism of a simple S(N)2 reaction, viz; OH(-) + CH(3)F = CH(3)OH + F(-) has been studied within the framework of reaction force and reaction electronic flux. We have computationally investigated three different types of reaction mechanisms with two different types of transition states, le...
  18. Mechanisms of formation of hemiacetals: intrinsic reactivity analysis.

    Journal of Physical Chemistry A: Molecules, Spe... 116(31):8250 (2012) PMID 22784613

    The reaction mechanism of the hemiacetal formation from formaldehyde and methanol has been studied theoretically at the B3LYP/6-311++G(d,p) level. In addition to the study of the reaction between the isolated reactants, three different kinds of catalysis have been explored. The first one examine...
  19. Understanding the physics and chemistry of reaction mechanisms from atomic contributions: a reaction force perspective.

    Journal of Physical Chemistry A: Molecules, Spe... 116(27):7419 (2012) PMID 22746292

    Studying chemical reactions involves the knowledge of the reaction mechanism. Despite activation barriers describing the kinetics or reaction energies reflecting thermodynamic aspects, identifying the underlying physics and chemistry along the reaction path contributes essentially to the overall...
  20. A relation between different scales of electrophilicity: are the scales consistent along a chemical reaction?

    Journal of Physical Chemistry A: Molecules, Spe... 116(26):7074 (2012) PMID 22630353

    In this paper, a relationship is established between three electrophilicity scales, namely, the electrophilicity index defined by Parr, Liu, and von Szentpaly; the electron affinity; and the energy of the lowest unoccupied molecular orbital (LUMO). Profiles of electrophilicity index and LUMO ene...