Repositorio Institucional Universidad EAFIT ::Examinando por Autor "David, Jorge"

Examinando por Autor "David, Jorge"

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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.
Electronic and Topological Analysis for New Phases of Chromium Nitride
(WILEY-V C H VERLAG GMBH, 2018-01-01) Marin-Suarez, Marco; Alzate-Vargas, Leidy L.; David, Jorge; Arroyave-Franco, Mauricio; Velez, Mario E.; Marin-Suarez, Marco; Alzate-Vargas, Leidy L.; David, Jorge; Arroyave-Franco, Mauricio; Velez, Mario E.; Universidad EAFIT. Departamento de Ciencias; Lógica y Computación
Chromium nitride (CrN) in its NaCl-type phase has been widely studied through density functional theory (DFT) in order to analyze its electronic properties. By the means of DFT with the Becke's three parameter Lee-Yang-Parr (B3LYP) hybrid functional, the same stoichiometry is studied in two unreported hypothetical phases in addition to the nonsynthesized and previously reported zinc-blende-type phase. The cohesive energy of every structure is calculated, and the analysis of this quantity indicated that all crystals are stable and that there is an unreported phase more stable than the synthesized one. The calculated electronic dispersion relation and density of electronic states allowed for the determination that these three phases have a conducting behavior. The symmetry of some bands is determined as a result of the crystal field splitting for chromium d states. The topology of the electron density was studied in order to determine its properties at bond critical points (BCPs). The form of the Laplacian of the density and its gradient trajectories allowed to locate ring critical points in these structures. From these calculations, it is concluded that all three phases are ionic crystals. The synthesized NaCl-type phase is studied in order to compare and confirm the results. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Electronic and Topological Analysis for New Phases of Chromium Nitride
(WILEY-V C H VERLAG GMBH, 2018-01-01) Marin-Suarez, Marco; Alzate-Vargas, Leidy L.; David, Jorge; Arroyave-Franco, Mauricio; Velez, Mario E.; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)
Chromium nitride (CrN) in its NaCl-type phase has been widely studied through density functional theory (DFT) in order to analyze its electronic properties. By the means of DFT with the Becke's three parameter Lee-Yang-Parr (B3LYP) hybrid functional, the same stoichiometry is studied in two unreported hypothetical phases in addition to the nonsynthesized and previously reported zinc-blende-type phase. The cohesive energy of every structure is calculated, and the analysis of this quantity indicated that all crystals are stable and that there is an unreported phase more stable than the synthesized one. The calculated electronic dispersion relation and density of electronic states allowed for the determination that these three phases have a conducting behavior. The symmetry of some bands is determined as a result of the crystal field splitting for chromium d states. The topology of the electron density was studied in order to determine its properties at bond critical points (BCPs). The form of the Laplacian of the density and its gradient trajectories allowed to locate ring critical points in these structures. From these calculations, it is concluded that all three phases are ionic crystals. The synthesized NaCl-type phase is studied in order to compare and confirm the results. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
(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.
Hydrophobic meddling in small water clusters
(SPRINGER, 2013-08-01) Hadad, C. Z.; Restrepo, Albeiro; Jenkins, Samantha; Ramirez, Frank; David, Jorge; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)
What would be the effects on the nature of hydrogen bonds, on the energies, and on the overall structural possibilities of replacing some hydrogen atoms by small hydrophobic groups in small water networks? Aiming at investigating this question, we performed an exhaustive search of the conformational space of the (Methanol)2(Water)3 representative model system, characterized the results, and made key comparative analysis with pentameric pure water clusters. The potential energy surface yielded a global minimum structural motif consisting of several puckered ring-like cyclic isomers very close in energy to each other. They are followed by other structural motifs, which, contrary to conventional belief, would also contribute to the properties of a macroscopic sample of this composition. We found that the C-H O interactions play a subordinate structural role and preferably accommodate to the established O-H O based structures. In comparison with the pure (H2O)5 case, we showed that (1) the same basic structural motifs and in a similar hierarchy energy order are obtained, but with a richer structural isomerism; (2) in general, the bonding is reinforced by the increase in the electrostatic and in the "degree of covalency" of the hydrogen-bonding components. Therefore, at least for this small cluster size, methyl groups slightly affect the structural isomerism and reinforce the hydrogen bonding. Additionally, we identified general factors of instability of the more unstable structures. © Springer-Verlag Berlin Heidelberg 2013.
Insights into the structure and stability of the carbonic acid dimer
(ROYAL SOC CHEMISTRY, 2010-01-01) Murillo, Juliana; David, Jorge; Restrepo, Albeiro; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)
In this paper we report the geometries and properties of 40 structural isomers located on the MP2/6-311++G** PES of the carbonic acid dimer. All six possible combinations of carbonic acid monomers were considered. The dimers are divided into six geometrical motifs. Our data suggests that combinations of anti-anti monomers do not necessarily lead to larger stabilization energies in the formation of the dimers. MP2 underestimates the relative binding energies with respect to CCSD(T) by as much as 3.2 kcal mol-1. At least 3 different dimers which may contribute to the stability of carbonic acid are predicted to have significant populations. Binding energy is only directly related to relative stability when comparing dimers formed from the same monomers. Overall stabilization is mainly dictated by attractive electrostatic interactions via cooperative polarization by virtue of the spatial arrangement of the dipole moment components along the polar bonds. Shorter O…H bond distances and larger bond orders predicted for the hydrogen bonds directed towards carbonyl groups make for stronger hydrogen bonding than in O…H bonds directed towards hydroxyl groups. © the Owner Societies.
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.
Microsolvation of dimethylphosphate: A molecular model for the interaction of cell membranes with water
(ROYAL SOC CHEMISTRY, 2013-01-01) Ibargueen, Cesar; Manrique-Moreno, Marcela; Hadad, C. Z.; David, Jorge; Restrepo, Albeiro; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)
We present an exhaustive stochastic search of the quantum conformational spaces of the (CH3O)2PO2 - + nH 2O (n = 1,2,3) systems. We uncover structural, conformational and energetic features of the problem. As in the isolated species, clusters containing the gauche-gauche (gg) conformation of dimethylphosphate (DMP -) are energetically preferred, however, contributions from hydrated gauche-anti (ga) and anti-anti (aa) monomers cannot be neglected because such structures are quite common and because they are close in energy to those containing the gg monomer. At least seven distinct types of O?H-O-H contacts lead to DMP- ? water interactions that are always stabilizing, but not strong enough to induce significant changes in the geometries of either DMP- or water units. Our results lead us to postulate DMP- to be a suitable model to study explicit and detailed aspects of microsolvation of cell membranes. This journal is © 2013 the Owner Societies.
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.
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.
Octahedral complexes of the series of actinides hexafluorides AnF 6
(ELSEVIER SCIENCE BV, 2011-04-29) Perez-Villa, Andrea; David, Jorge; Fuentealba, Patricio; Restrepo, Albeiro; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)
Non-relativistic DFT (PW91, PBE, PB86) geometry optimizations followed by relativistic ZORA single point energy calculations on the neutral hexafluoride complexes of the series of actinides U, Np, Pu, Am, Cm, Bk, Cf, Es, Fm, Md, No, Lr in octahedral symmetry are presented. Bond lengths are in good agreement with available experimental data. Actinide bond length contraction as a function of the atomic number of the central metal atom of up to ˜4% is observed. An approximate inverse relationship is predicted for the bonding energies as a function of the atomic number of the central cation at the two component ZORA//DFT level; pure DFT bonding energies do not exhibit the same pattern. © 2011 Elsevier B.V. All rights reserved.
Spanning QTAIM topology phase diagrams of water isomers W4, W5 and W6
(ROYAL SOC CHEMISTRY, 2011-01-01) Jenkins, Samantha; Restrepo, Albeiro; David, Jorge; Yin, Dulin; Kirk, Steven R.; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)
Structural and chemical properties of the small water clusters W 4, W5 and W6 are investigated with the theory of atoms and molecules (QTAIM). For the W4, W5 and W 6 clusters, nine, fourteen and twenty-seven conformers, respectively, have been analyzed. For the W4, W5 and W6 clusters one, two and three of these structures, respectively, have not been reported before. We then proceed to extend the W4, W5 and W6 water cluster topology space using QTAIM; the PoincaréHopf topological sum rules are applied to create rules to identify the spanning set of conformer topologies, this includes finding three, ten and eight new distinct topologies that satisfy the PoincaréHopf relation for W4, W5 and W6 respectively. The topological stability of degenerate solutions to the PoincaréHopf relation is compared by evaluating the proximity to rupturing of critical points of the gradient vector field of the charge density. We introduce a QTAIM topology space to replace the inconsistent use of Euclidean geometry to determine whether a cluster is 1-, 2- or 3-D. We show from the topology of the charge density that the conformers of the W 4, W5 clusters are more energetically stable in less compact, planar forms, conversely the conformers of W6 are more energetically stable with compact 3-D topologies. Quantifying the degree of covalent character in the hydrogen bonding for the W4, W5 and W6 clusters independently verifies this finding. Differences in simple rules for the number of hydrogen bonds obeying the BernalFowler ice rules between W4, W5 and W6 reflect the transition from 2-D to 3-D structures being more energetically stable. In addition, we identify a new class of OO bonding interactions that are up to 48% longer than the inter-nuclear separation and appear to be failed hydrogen bonds. © 2011 the Owner Societies.
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.
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.
Structural studies of the water hexamer
(AMER CHEMICAL SOC, 2010-07-29) Hincapie, Gina; Acelas, Nancy; Castano, Marcela; David, Jorge; Restrepo, Albeiro; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)
In this paper we report the geometries and properties of 24 structural isomers located on the MP2/6-311++g**potential energy surface of the water hexamer. At least 15 structural patterns are located within 3 kcal/mol of the most stable conformation, leading to a very complex potential energy surface, several isomers having significant contributions. A quadratic correlation between the distance from the proton to the center of the hydrogen bond with the distance between oxygen atoms for all clusters is reported. MP2/6-311++g**and CCSD(T)/aug-cc-pvdz//MP2/6-311++g**predict different stabilization orderings but are in good agreement for binding energies. Compact structures are energetically favored by electronic energies with zero point energy corrections, while noncompact cyclic structures are preferred when temperature and entropy are accounted for. © 2010 American Chemical Society.
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.
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.
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.
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.
Understanding microsolvation of Li+: Structural and energetical analyses
(ROYAL SOC CHEMISTRY, 2011-09-07) Romero, Jonathan; Reyes, Andres; David, Jorge; Restrepo, Albeiro; Universidad EAFIT. Departamento de Ciencias Básicas; Electromagnetismo Aplicado (Gema)
A stochastic exploration of the quantum conformational space for the (H2O)nLi+, n = 3, 4, 5 complexes produced 32 molecular clusters at the B3LYP/6-311++G** and MP2/6- 311++G** levels. The first solvation shell is predicted to comprise a maximum of 4 water molecules. Energy decomposition analyses were performed to determine the relationship between the geometrical features of the complexes and the types of interactions responsible for their stabilization. Our findings reveal that electrostatic interactions are major players determining the structures and relative stabilities of the clusters. The formal charge on the Li atom leads to two distinct types of hydrogen bonds, scattered in a wide range of distances (1.61-2.32 Å), in many cases affording H-bonds that are considerably larger and considerably shorter than those in pure water clusters (typically ~1.97 Å). © 2011 The Owner Societies.

Examinando por Autor "David, Jorge"

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