Examinando por Autor "Guerra, Doris"
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Ítem Density functional based reactivity parameters: Thermodynamic or kinetic concepts?(ELSEVIER SCIENCE BV, 2010-03-15) Fuentealba, Patricio; David, Jorge; Guerra, Doris; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)The Density Functional Theory of chemical reactivity has provided and effective way to develop a mathematical framework for many empirical chemical concepts. In this work, the relation of some of the proposed indexes with the thermodynamic and kinetic effects on a chemical reaction will be discussed. In order to give a numerical support to the discussion, families of SN2 reactions and Diels-Alder reactions have been studied. It is concluded that the theoretical proposed indexes represent neither thermodynamic nor kinetic effects but a combination of both depending on the type of reaction. © 2009 Elsevier B.V. All rights reserved.Ítem (H 3N-BH 3) 4: The ammonia borane tetramer(ROYAL SOC CHEMISTRY, 2012-01-01) Guerra, Doris; David, Jorge; Restrepo, Albeiro; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)For this special edition of PCCP dealing with prediction of new molecules using quantum mechanical methods, we propose a structure for (H 3N-BH 3) 4, the isolated ammonia borane tetramer in gas phase, for which there are no experimental reports. The structure, belonging to the S 4 point group, was found at the MP2/6-311++G(d,p) level of theory; the total energy was computed at the CCSD(T) level including BSSE correction, affording a binding energy of 40.1 kcal mol -1. The tetramer is stabilized by a network of dihydrogen bonds. We study the stabilizing interactions via QTAIM, obtaining eight N-H d+? d-H-B bonding interactions characterized as hydrogen bonds by application of the Koch-Popelier rules; in addition, two highly controversial B-H d-? d-H-B interactions are also predicted by a topological analysis of the electron density. This journal is © 2012 the Owner Societies.Ítem The Jahn-Teller effect: a case of incomplete theory for d4 complexes?(AMER CHEMICAL SOC, 2011-02-21) David, Jorge; Guerra, Doris; Restrepo, Albeiro; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)We present relativistic calculations at the four-component Dirac-DFT level for the geometries of the series of group 9 monoanionic hexafluorides MF(6)(-), M = Co, Rh, Ir. Highly correlated four-component relativistic CCSD(T) energies were also calculated for the optimized geometries. Spin-orbit coupling effects influence the geometrical preferences for molecular structures: relativistic calculations predict ground states with octahedral symmetries O(h)* for all hexafluorides in this study, while at the nonrelativistic limit, a structural deviation toward D(4h) ground state symmetries is predicted. Our findings suggest that relativistic effects have an important role in molecular structure preferences for the title hexafluorides.Ítem New stable phases of glycine crystals(Elsevier BV, 2020-02-01) Guerra, Doris; Gomez, Luis A.; Restrepo, Albeiro; David, Jorge; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)A Density Functional Theory (DFT) study of the electronic, energetic, dynamical, and mechanical properties of new glycine molecular crystals is presented here. Our search of the potential energy surface (PES) reproduces the previously reported structures for alpha-, beta-, and gamma-glycine with P2(1/n), P2(1), P3(1) symmetries, respectively. In addition, we report three new orthorhombic (o), tetragonal (t), and monoclinic (m) crystals with P2(1)2(1)2(1), P4(3), and P2(1) symmetries. The crystals have wide band gaps, classifying them in the range of insulators. All three new phases have low mechanical hardness (< 3.2 GPa), characterizing them as soft crystals. Topological and local energetic properties of the electronic densities for the new crystalline phases of glycine have been calculated using the tools provided by the quantum theory of atoms in molecules (QTAIM) under periodic conditions. Typical NH center dot center dot center dot O, OH center dot center dot center dot O as well as secondary CH center dot center dot center dot O hydrogen bonds (HBs), act as the stabilizing factors resulting in large cohesive energies for the new phases of glycine crystals. Without exception, all types of HBs, for all new phases, perfectly fit the attractive region of a Lennard-Jones potential.Ítem New stable phases of glycine crystals(Elsevier BV, 2020-02-01) Guerra, Doris; Gomez, Luis A.; Restrepo, Albeiro; David, Jorge; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)A Density Functional Theory (DFT) study of the electronic, energetic, dynamical, and mechanical properties of new glycine molecular crystals is presented here. Our search of the potential energy surface (PES) reproduces the previously reported structures for alpha-, beta-, and gamma-glycine with P2(1/n), P2(1), P3(1) symmetries, respectively. In addition, we report three new orthorhombic (o), tetragonal (t), and monoclinic (m) crystals with P2(1)2(1)2(1), P4(3), and P2(1) symmetries. The crystals have wide band gaps, classifying them in the range of insulators. All three new phases have low mechanical hardness (< 3.2 GPa), characterizing them as soft crystals. Topological and local energetic properties of the electronic densities for the new crystalline phases of glycine have been calculated using the tools provided by the quantum theory of atoms in molecules (QTAIM) under periodic conditions. Typical NH center dot center dot center dot O, OH center dot center dot center dot O as well as secondary CH center dot center dot center dot O hydrogen bonds (HBs), act as the stabilizing factors resulting in large cohesive energies for the new phases of glycine crystals. Without exception, all types of HBs, for all new phases, perfectly fit the attractive region of a Lennard-Jones potential.Ítem Structural characterization of the (MeSH)4 potential energy surface(SPRINGER, 2013-05-01) Gomez, Sara; Guerra, Doris; David, Jorge; Restrepo, Albeiro; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)A random walk on the PES for (MeSH)4 clusters produced 50 structural isomers held together by hydrogenbonding networks according to calculations performed at the B3LYP/6-311++G* * andMP2/6-311++G* * levels. The geometric motifs observed are somewhat similar to those encountered for the methanol tetramer, but the interactions responsible for cluster stabilization are quite different in origin. Cluster stabilization is not related to the number of hydrogen bonds. Two distinct, well-defined types of hydrogen bonds scattered over a wide range of distances are predicted. © Springer-Verlag Berlin Heidelberg 2012.Ítem Structural characterization of the (methanol)4 potential energy surface(AMER CHEMICAL SOC, 2009-09-24) David, Jorge; Guerra, Doris; Restrepo, Albeiro; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)In this paper, we report the geometries and properties of the structural isomers obtained from a random walk of the potential energy surface (PES) of the methanol tetramer. Thirty-three structures were obtained after B3LYP/6-31+g* optimization of 94 candidate structures generated from a stochastic search of the PM3 conformational space. The random search was carried out using a recently proposed modified Metropolis acceptance test in the simulated annealing (SA) procedure. Corrections for the basis set superposition error (BSSE) show improvements on the binding energies of the clusters in an average of approximately 2.0 kcal/mol, while geometries are predicted to be less sensitive to BSSE corrections. MP2/aug-cc-pvdz calculations on representative structures did not change the geometries but predicted better binding energies. Highly correlated CCSD(T) energies were calculated on the B3LYP and MP2 stationary points and used to establish relative stabilities. We report several new conformations and group the structures into six distinct geometrical motifs. Only the cyclic tetramers with four primary hydrogen bonds in the same plane are predicted to have significant populations. Secondary hydrogen bonds, those for which the donated proton comes from an alkyl group, lead to a rich conformational space.Ítem Structural studies of the water pentamer(ELSEVIER SCIENCE BV, 2011-05-09) Ramirez, Frank; Hadad, C. Z.; Guerra, Doris; David, Jorge; Restrepo, Albeiro; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)A computational study of the water pentamer gas phase conformational space is reported in this Letter. Forty-four stationary points distributed among 12 structural patterns were located at the MP2/6-311++G(d,p) level. At least 5 geometrical motifs (25 structures) are predicted within 3 kcal/mol of the most stable conformation at the CCSD(T)/aug-cc-pVTZ//MP2/6-311++G(d,p) level. We show evidence that dipole-dipole interactions are at play in stabilizing the clusters. Electron densities and their Laplacians at the hydrogen bond critical points were found to be linearly correlated with relative energies for all clusters. Logarithmic relationships were found for the [req, ?(rc)] and [req,?2?( rc)] pairs in all hydrogen bonds. © 2011 Elsevier B.V. All rights reserved.Ítem Structure and reactivity of the (1)Au6Pt clusters(AMER CHEMICAL SOC, 2010-10-07) David, Jorge; Guerra, Doris; Hadad, C. Z.; Restrepo, Albeiro; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)In this paper we report the geometries, properties, and reactivity descriptors of 12 structural isomers located on the MP2/SDDALL potential energy surface of the (1)Au(6)Pt binary clusters. A nonplanar, D(3d) symmetry, cyclohexane chairlike structure is predicted to be the global minimum. Binding energies per atom in the range approximately 44-51 kcal/mol account for very stable clusters. The relative stability of the clusters is directly related to all global and local reactivity descriptors. All structures are predicted to have large electron affinities. The chemical environment of the Pt atom on the structures plays a central role in the resulting relative stabilities and global and local reactivities. Our results show that more peripheral Pt atoms are more likely to be involved in electron-accepting processes.Ítem Structure, stability and bonding in the 1Au 10 clusters(ELSEVIER SCIENCE BV, 2012-06-29) David, Jorge; Guerra, Doris; Restrepo, Albeiro; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)A stochastic exploration of the quantum conformational space for the 1Au 10 system using a modified Metropolis acceptance test afforded 15 stable configurations in the MP2/SDDALL potential energy surface. The global minimum is predicted to be a 3D structure with D2 d symmetry. Topological analyses of the electron densities suggest that bonding appears to be of intermediate character, with substantial contributions from both covalent and closed shell interactions and that there is a direct correlation between the topological complexity of the electron density and cluster stability. Evidence regarding the nature of the interactions is gathered from many sources, including the total number of delocalized electrons (nde), a novel covalency index. Localization indices and condensed Fukui functions predict higher electron populations on peripheral, lowly coordinated atoms. © 2012 Elsevier B.V. All rights reserved.Ítem Structures, energies, and bonding in the water heptamer(AMER INST PHYSICS, 2013-07-28) Acelas, Nancy; Hincapie, Gina; Guerra, Doris; David, Jorge; Restrepo, Albeiro; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)In this paper we report the geometries and properties of 38 distinct geometrical motifs located on the B3LYP/6-31+G(d), MP2/6-311++G(d, p) potential energy surfaces of the water heptamer. Binding energies of up to 45 kcal/mol are calculated. All motifs fall within 10 kcal/mol of the most stable conformation, with at least 13 structural patterns located no more than 3 kcal/mol above, leading to a very complex potential energy surface, populated by a multitude of motifs each one allowing large numbers of conformations. Cluster stability does not seem to be correlated with the number of hydrogen bonds. Compact structures are energetically favored by electronic energies with zero-point energy corrections, while more open structures are preferred when temperature and entropy are accounted for. The molecular interactions holding the clusters as discrete units lead to large binding energies but are not strong enough to cause significant changes in the geometries of the interacting monomers. Our results indicate that bonding in the water heptamers can be considered as largely non-shared interactions with contributions from intermediate character of increasing covalency. © 2013 AIP Publishing LLC.