2014 |
Gallardo-Fuentes, S; Tapia, R A; Contreras, R; Campodonico, P R Site Activation Effects Promoted by Intramolecular Hydrogen Bond Interactions in Snar Reactions Artículo de revista Rsc Advances, 4 (58), pp. 30638-30643, 2014, ISSN: 2046-2069. Resumen | Enlaces | BibTeX | Etiquetas: aromatic electrophilicity, functionals, markovnikov model molecules, nucleophilic-substitution, potentials, reactivity, regioselectivity rule, secondary-amines, solvent @article{RN225, title = {Site Activation Effects Promoted by Intramolecular Hydrogen Bond Interactions in Snar Reactions}, author = { S. Gallardo-Fuentes and R.A. Tapia and R. Contreras and P.R. Campodonico}, url = {/brokenurl#<Go to ISI>://WOS:000340500300025}, doi = {10.1039/c4ra04725g}, issn = {2046-2069}, year = {2014}, date = {2014-01-01}, journal = {Rsc Advances}, volume = {4}, number = {58}, pages = {30638-30643}, abstract = {The nucleophilic aromatic substitution reaction of benzohydrazide derivatives towards 2-chloro-5nitropyrimidine is used as model system to experimentally and theoretically show that intramolecular hydrogen-bond formation operates as a perturbation that elicits a dual response at the reaction center of the transition state (TS) structure, by enhancing the electrophilicity of the pyrimidine moiety and the nucleophilicity of the nitrogen atom of the benzohydrazide fragment. The electronic mechanism can therefore be described as a (non-local) site activation problem.}, keywords = {aromatic electrophilicity, functionals, markovnikov model molecules, nucleophilic-substitution, potentials, reactivity, regioselectivity rule, secondary-amines, solvent}, pubstate = {published}, tppubtype = {article} } The nucleophilic aromatic substitution reaction of benzohydrazide derivatives towards 2-chloro-5nitropyrimidine is used as model system to experimentally and theoretically show that intramolecular hydrogen-bond formation operates as a perturbation that elicits a dual response at the reaction center of the transition state (TS) structure, by enhancing the electrophilicity of the pyrimidine moiety and the nucleophilicity of the nitrogen atom of the benzohydrazide fragment. The electronic mechanism can therefore be described as a (non-local) site activation problem. |
2012 |
Soto-Delgado, J; Aizman, A; Contreras, R; Domingo, L R On the Catalytic Effect of Water in the Intramolecular Diels-Alder Reaction of Quinone Systems: A Theoretical Study Artículo de revista Molecules, 17 (11), pp. 13687-13703, 2012, ISSN: 1420-3049. Resumen | Enlaces | BibTeX | Etiquetas: catalysis, characterization, chemistry density dft dft, diels-alder difference electrophilicity, functionals, index, indices, intramolecular local molecules, polar quantitative reactions, reactivity regioselectivity, solvent, thermochemistry, water @article{sotodelgado2012catalytic, title = {On the Catalytic Effect of Water in the Intramolecular Diels-Alder Reaction of Quinone Systems: A Theoretical Study}, author = { J. Soto-Delgado and A. Aizman and R. Contreras and L.R. Domingo}, url = {/brokenurl#<Go to ISI>://WOS:000311428400087}, doi = {10.3390/molecules171113687}, issn = {1420-3049}, year = {2012}, date = {2012-01-01}, journal = {Molecules}, volume = {17}, number = {11}, pages = {13687-13703}, abstract = {The mechanism of the intramolecular Diels-Alder (IMDA) reaction of benzoquinone 1, in the absence and in the presence of three water molecules, 1w, has been studied by means of density functional theory (DFT) methods, using the M05-2X and B3LYP functionals for exploration of the potential energy surface (PES). The energy and geometrical results obtained are complemented with a population analysis using the NBO method, and an analysis based on the global, local and group electrophilicity and nucleophilicity indices. Both implicit and explicit solvation emphasize the increase of the polarity of the reaction and the reduction of activation free energies associated with the transition states (TSs) of this IMDA process. These results are reinforced by the analysis of the reactivity indices derived from the conceptual DFT, which show that the increase of the electrophilicity of the quinone framework by the hydrogen-bond formation correctly explains the high polar character of this intramolecular process. Large polarization at the TSs promoted by hydrogen-bonds and implicit solvation by water together with a high electrophilicity-nucleophilicity difference consistently explains the catalytic effects of water molecules.}, keywords = {catalysis, characterization, chemistry density dft dft, diels-alder difference electrophilicity, functionals, index, indices, intramolecular local molecules, polar quantitative reactions, reactivity regioselectivity, solvent, thermochemistry, water}, pubstate = {published}, tppubtype = {article} } The mechanism of the intramolecular Diels-Alder (IMDA) reaction of benzoquinone 1, in the absence and in the presence of three water molecules, 1w, has been studied by means of density functional theory (DFT) methods, using the M05-2X and B3LYP functionals for exploration of the potential energy surface (PES). The energy and geometrical results obtained are complemented with a population analysis using the NBO method, and an analysis based on the global, local and group electrophilicity and nucleophilicity indices. Both implicit and explicit solvation emphasize the increase of the polarity of the reaction and the reduction of activation free energies associated with the transition states (TSs) of this IMDA process. These results are reinforced by the analysis of the reactivity indices derived from the conceptual DFT, which show that the increase of the electrophilicity of the quinone framework by the hydrogen-bond formation correctly explains the high polar character of this intramolecular process. Large polarization at the TSs promoted by hydrogen-bonds and implicit solvation by water together with a high electrophilicity-nucleophilicity difference consistently explains the catalytic effects of water molecules. |
Bernales, V S; Marenich, A V; Contreras, R; Cramer, C J; Truhlar, D G Quantum Mechanical Continuum Solvation Models for Ionic Liquids Artículo de revista Journal of Physical Chemistry B, 116 (30), pp. 9122-9129, 2012, ISSN: 1520-6106. Resumen | Enlaces | BibTeX | Etiquetas: ab-initio, approach, carbon-dioxide, density dielectric-constant, free-energies, functionals, gas-phase green kinetics, molecular-dynamics simulations, solvents, static thermochemical universal @article{RN105, title = {Quantum Mechanical Continuum Solvation Models for Ionic Liquids}, author = { V.S. Bernales and A.V. Marenich and R. Contreras and C.J. Cramer and D.G. Truhlar}, url = {/brokenurl#<Go to ISI>://WOS:000306989800043}, doi = {10.1021/jp304365v}, issn = {1520-6106}, year = {2012}, date = {2012-01-01}, journal = {Journal of Physical Chemistry B}, volume = {116}, number = {30}, pages = {9122-9129}, abstract = {The quantum mechanical SMD continuum universal solvation model can be applied to predict the free energy of solvation of any solute in any solvent following specification of various macroscopic solvent parameters. For three ionic liquids where these descriptors are readily available, the SMD solvation model exhibits a mean unsigned error of 0.48 kcal/mol for 93 solvation free energies of neutral solutes and a mean unsigned error of 1.10 kcal/mol for 148 water-to-IL transfer free energies. Because the necessary solvent parameters are not always available for a given ionic liquid, we determine average values for a set of ionic liquids over which measurements have been made in order to define a generic ionic liquid solvation model, SMD-GIL. Considering 11 different ionic liquids, the SMD-GIL solvation model exhibits a mean unsigned error of 0.43 kcal/mol for 344 solvation free energies of neutral solutes and a mean unsigned error of 0.61 kcal/mol for 431 water-to-IL transfer free energies. As these errors are similar in magnitude to those typically observed when applying continuum solvation models to ordinary liquids, we conclude that the SMD universal solvation model may be applied to ionic liquids as well as ordinary liquids.}, keywords = {ab-initio, approach, carbon-dioxide, density dielectric-constant, free-energies, functionals, gas-phase green kinetics, molecular-dynamics simulations, solvents, static thermochemical universal}, pubstate = {published}, tppubtype = {article} } The quantum mechanical SMD continuum universal solvation model can be applied to predict the free energy of solvation of any solute in any solvent following specification of various macroscopic solvent parameters. For three ionic liquids where these descriptors are readily available, the SMD solvation model exhibits a mean unsigned error of 0.48 kcal/mol for 93 solvation free energies of neutral solutes and a mean unsigned error of 1.10 kcal/mol for 148 water-to-IL transfer free energies. Because the necessary solvent parameters are not always available for a given ionic liquid, we determine average values for a set of ionic liquids over which measurements have been made in order to define a generic ionic liquid solvation model, SMD-GIL. Considering 11 different ionic liquids, the SMD-GIL solvation model exhibits a mean unsigned error of 0.43 kcal/mol for 344 solvation free energies of neutral solutes and a mean unsigned error of 0.61 kcal/mol for 431 water-to-IL transfer free energies. As these errors are similar in magnitude to those typically observed when applying continuum solvation models to ordinary liquids, we conclude that the SMD universal solvation model may be applied to ionic liquids as well as ordinary liquids. |
Mera-Adasme, R; Mendizabal, F; González, M; Miranda-Rojas, S; Olea-Azar, C; Sundholm, D Computational Studies of the Metal-Binding Site of the Wild-Type and the H46r Mutant of the Copper, Zinc Superoxide Dismutase Artículo de revista Inorganic Chemistry, 51 (10), pp. 5561-5568, 2012, ISSN: 0020-1669. Resumen | Enlaces | BibTeX | Etiquetas: amyotrophic-lateral-sclerosis, approximation, correlation-energy, crystal-structures, cu, density efficient, functionals, sod1, solvents zn @article{RN85, title = {Computational Studies of the Metal-Binding Site of the Wild-Type and the H46r Mutant of the Copper, Zinc Superoxide Dismutase}, author = { R. Mera-Adasme and F. Mendizabal and M. Gonz\'{a}lez and S. Miranda-Rojas and C. Olea-Azar and D. Sundholm}, url = {/brokenurl#<Go to ISI>://WOS:000304215200011}, doi = {10.1021/ic202416d}, issn = {0020-1669}, year = {2012}, date = {2012-01-01}, journal = {Inorganic Chemistry}, volume = {51}, number = {10}, pages = {5561-5568}, abstract = {Impairment of the Zn(II)-binding site of the copper, zinc superoxide dismutase (CuZnSOD) protein is involved in a number of hypotheses and explanations for the still unknown toxic gain of function mutant varieties of CuZnSOD that are associated with familial forms of amyotrophic lateral sclerosis (ALS). In this work, computational chemistry methods have been used for studying models of the metal-binding site of the ALS-linked H46R mutant of CuZnSOD and of the wild-type variety of the enzyme. By comparing the energy and electronic structure of these models, a plausible explanation for the effect of the H46R mutation on the zinc site is obtained. The computational study clarifies the role of the D124 and D125 residues for keeping the structural integrity of the Zn(II)-binding site, which was known to exist but its mechanism has not been explained. Earlier results suggest that the explanation for the impairment of the Zn(II)-site proposed in this work may be useful for understanding the mechanism of action of the ALS-linked mutations in CuZnSOD in general.}, keywords = {amyotrophic-lateral-sclerosis, approximation, correlation-energy, crystal-structures, cu, density efficient, functionals, sod1, solvents zn}, pubstate = {published}, tppubtype = {article} } Impairment of the Zn(II)-binding site of the copper, zinc superoxide dismutase (CuZnSOD) protein is involved in a number of hypotheses and explanations for the still unknown toxic gain of function mutant varieties of CuZnSOD that are associated with familial forms of amyotrophic lateral sclerosis (ALS). In this work, computational chemistry methods have been used for studying models of the metal-binding site of the ALS-linked H46R mutant of CuZnSOD and of the wild-type variety of the enzyme. By comparing the energy and electronic structure of these models, a plausible explanation for the effect of the H46R mutation on the zinc site is obtained. The computational study clarifies the role of the D124 and D125 residues for keeping the structural integrity of the Zn(II)-binding site, which was known to exist but its mechanism has not been explained. Earlier results suggest that the explanation for the impairment of the Zn(II)-site proposed in this work may be useful for understanding the mechanism of action of the ALS-linked mutations in CuZnSOD in general. |
2014 |
Site Activation Effects Promoted by Intramolecular Hydrogen Bond Interactions in Snar Reactions Artículo de revista Rsc Advances, 4 (58), pp. 30638-30643, 2014, ISSN: 2046-2069. |
2012 |
On the Catalytic Effect of Water in the Intramolecular Diels-Alder Reaction of Quinone Systems: A Theoretical Study Artículo de revista Molecules, 17 (11), pp. 13687-13703, 2012, ISSN: 1420-3049. |
Quantum Mechanical Continuum Solvation Models for Ionic Liquids Artículo de revista Journal of Physical Chemistry B, 116 (30), pp. 9122-9129, 2012, ISSN: 1520-6106. |
Computational Studies of the Metal-Binding Site of the Wild-Type and the H46r Mutant of the Copper, Zinc Superoxide Dismutase Artículo de revista Inorganic Chemistry, 51 (10), pp. 5561-5568, 2012, ISSN: 0020-1669. |