Josefredo Pliego | UFSJ - Federal University of São João Del-Rei (original) (raw)
Papers by Josefredo Pliego
Química Nova
SCIENTISTS’ ASSESSMENT: ARE WE USING THE CORRECT METRICS? The use of metrics to evaluate scientis... more SCIENTISTS’ ASSESSMENT: ARE WE USING THE CORRECT METRICS? The use of metrics to evaluate scientists is widespread in the present time, with implications for hiring, fellowships, and research grants. Such fact requires that metrics must be constantly scrutinized to be improved. This work analyzes the use of metrics in the area of chemistry in Brazil and discusses its limitations and shortcomings. The main findings indicate that the use of the impact factor must be complemented by the cited half-life of the journals, and a composite metric named influence factor is proposed, similar to the R-impact. The h-index is not a good metric anymore because does not correct for authorship inflation. The individual h-index (hi), which takes into account fractional counting of citations, is more reliable than the h-index. An analysis on the use of hi-index with randomly selected 15 Brazilian chemists among the top 500 more productive shows an important effect on the ranking order.
Journal of the Brazilian Chemical Society
The classical alkylation reaction of benzene with isopropyl chloride catalyzed by the species AlC... more The classical alkylation reaction of benzene with isopropyl chloride catalyzed by the species AlCl3 and Al2Cl6 was studied using reliable calculations at M06-2X/def2-TZVPP//X3LYP/def2/SVP level of theory and SMD model for solvent effect. We evaluated the formation of dimers, trimers, tetramers, and pentamers and showed that Al2Cl6 dimers exist in greater proportion, in agreement with experimental observations. The experimental solubility of Al2Cl6 in benzene was also included in the theoretical kinetics analysis. The reaction catalyzed by AlCl3 species presents the highest barrier, in part due to unfavorable dissociation of the Al2Cl6 species. The mechanism via Al2Cl6 catalysis is more effective and even considering its low solubility, the calculated observed ΔG‡ is only 20.6 kcal mol-1, indicating a fast reaction rate. The mechanism involves the formation of the CH3CHCH3+…Al2Cl7− ion pair, which reacts with benzene to form a Wheland intermediate and this carbon-carbon bond formatio...
Journal of Molecular Modeling
RSC Advances, 2016
A reliable theoretical calculation of the free energy profile of a base-catalyzed Knoevenagel rea... more A reliable theoretical calculation of the free energy profile of a base-catalyzed Knoevenagel reaction shows that hydroxide ion elimination step is rate determining.
Journal of the Chemical Society-Perkin Transactions 2, 2000
ABSTRACT
Química Nova, 2016
BUILDING THE LIQUID-VAPOUR EQUILIBRIUM CURVE THROUGH A CUBIC EQUATION OF STATE: USE OF EXCEL FOR ... more BUILDING THE LIQUID-VAPOUR EQUILIBRIUM CURVE THROUGH A CUBIC EQUATION OF STATE: USE OF EXCEL FOR TEACHING PHYSICAL-CHEMISTRY. Cubic equations of state are able to predict the liquid-vapour coexistence curve of volatile substances. However, this property is rarely used to teach Physical Chemistry because solving the resulting equations require numerical technics and many mathematical operations. In this report was shown how the interactive method for finding the root of an equation can be applied with the Excel to determine the vapour pressure of the liquid, as well as the molar volumes of the gas and liquid phases. The generated points was used to build the curves of phase transition in the P × V and P × T graphics.
Theoretical Chemistry Accounts, 2014
ABSTRACT
Physical Chemistry Chemical Physics
Accurate calculation of the solvation free energy of single ions remains an important goal, invol... more Accurate calculation of the solvation free energy of single ions remains an important goal, involving the development in the dielectric continuum solvation models, statistical mechanics with explicit solvent and hybrid...
Asian Journal of Organic Chemistry
Arkivoc
Theoretical modeling of the formation imines in aqueous medium from the reaction of amines with a... more Theoretical modeling of the formation imines in aqueous medium from the reaction of amines with aldehydes is difficult due to formation of charged species, zwitterions, acid-base equilibria and a substantial solvent effect. In this work, a model reaction of methylamine with acetaldehyde was investigated involving neutral and ionic pathways, influence of the pH and different approaches for treating the solvent effect. We have found a mechanism able to explain the fast kinetics of this system, involving the zwitterion formation followed by its isomerization to the carbinolamine and an easy iminium ion formation via an ionic elimination mechanism.
Journal of the Brazilian Chemical Society, 2016
In the past seven years, the SMD (Solvent Model Density) method has been widely used by computati... more In the past seven years, the SMD (Solvent Model Density) method has been widely used by computational chemists. Thus, assessment on the reliability of this model for modeling chemical process in solution is worthwhile. In this report, it was investigated six anion-molecule nucleophilic substitution reactions in methanol and dipolar aprotic solvents. Geometry optimizations have been done at SMD/X3LYP level and single point energy calculations at CCSD(T)/TZVPP + diff level. Our results have indicated that the SMD model is not adequate for dipolar aprotic solvents, with a root of mean squared (RMS) error of 5.6 kcal mol-1 , while the Polarizable Continuum Model (PCM) method with the Pliego and Riveros atomic cavities has led to RMS error of only 3.2 kcal mol-1. For methanol solvent, the SMD method has a RMS error of 3.0 kcal mol-1. The classical protic to dipolar aprotic solvent rate acceleration effect was not predicted by the SMD model for the tested systems.
Química Nova
FORMATION OF AZEOTROPES FROM THE STANDPOINT OF SOLVATION THERMODYNAMICS. The formation of azeotro... more FORMATION OF AZEOTROPES FROM THE STANDPOINT OF SOLVATION THERMODYNAMICS. The formation of azeotropes is related to the deviation of the ideality of liquid mixtures. This deviation is expressed by the activity coefficient of each component. However, the physical origin of this behavior is not well quantified in terms of molecular interactions. In this work, a regular solution model was used, relating the β parameter to the solvation free energy of pure liquids in themselves and in the other component. A mathematical expression was derived that indicates when an azeotrope is formed. This equation shows that the greater the difference in vapour pressure between components, the greater the solvation difference of each liquid in itself and in the other component is needed to form the azeotrope. A set of 10 mixtures were randomly chosen and investigated as a test, and the equation worked in all cases.
Computational and Theoretical Chemistry
Organic & Biomolecular Chemistry
A general view of the medium effects on ionic reactions involves the solvent effect, ion pairing,... more A general view of the medium effects on ionic reactions involves the solvent effect, ion pairing, formation of aggregates and structured environment.
Molecular Systems Design & Engineering
A new macrocycle combining thiourea and crown ether groups is able to solubilize KF and promote f... more A new macrocycle combining thiourea and crown ether groups is able to solubilize KF and promote fluorination via stabilization of the SN2 transition state via four hydrogen bonds.
Physical Chemistry Chemical Physics
Amino-thiourea organocatalysis is an important catalytic process for enantioselective conjugate a... more Amino-thiourea organocatalysis is an important catalytic process for enantioselective conjugate addition reactions.
Theoretical Chemistry Accounts
Anion-molecule reactions have a substantial solvent effect, which decreases with the solvent pola... more Anion-molecule reactions have a substantial solvent effect, which decreases with the solvent polarity. However, less solvation leads to the formation of ion pairs and higher aggregates that are usually less reactive. Consequently, theoretical determination of the best solvent for the reaction needs to consider all the species in equilibrium. In this report, we have investigated the wide range of solvent polarity in the S N Ar reaction of the tetramethylammonium fluoride (TMAF) with 2-bromobenzonitrile, as well as the formation of ion pairs, dimers and tetramers using molecular dynamics and density functional calculations with continuum solvation. Five solvents were considered: methanol, dimethylformamide, pyridine, tetrahydrofuran and benzene. The TMAF exists predominantly as free ions in methanol, as ion pairs in dimethylformamide and pyridine, and as tetramers in tetrahydrofuran and benzene. The reaction takes place through free ions in methanol, ion pairs in dimethylformamide, pyridine and tetrahydrofuran, and via dimer in benzene. The calculations suggest that dimethylformamide and pyridine are the best solvents for this reaction.
Química Nova
Finding the most efficient solvent for a chemical reaction can demand costly experimental procedu... more Finding the most efficient solvent for a chemical reaction can demand costly experimental procedure and the screening is usually limited to few solvents. The use of theoretical methods could accelerate the search for the best solvent, able to promote most effective kinetics and thermodynamics of a reaction. In this work, it was proposed an automated procedure that calculates the solvent effect for a chemical reaction using all the 179 solvents available in SMD (solvation model density). The reaction of 2-bromoacetophenone with pyridine was used as a test. The SMD model correctly predicts the reactivity trends for five solvents, which experimental data are available. We have found that sulfolane, a less usual solvent, is the best one for this reaction. The present study points out that computational screening of large set of solvents using the SMD model is a viable approach and could be useful for chemical reactions optimization.
International Journal of Quantum Chemistry
Journal of Molecular Modeling
Química Nova
SCIENTISTS’ ASSESSMENT: ARE WE USING THE CORRECT METRICS? The use of metrics to evaluate scientis... more SCIENTISTS’ ASSESSMENT: ARE WE USING THE CORRECT METRICS? The use of metrics to evaluate scientists is widespread in the present time, with implications for hiring, fellowships, and research grants. Such fact requires that metrics must be constantly scrutinized to be improved. This work analyzes the use of metrics in the area of chemistry in Brazil and discusses its limitations and shortcomings. The main findings indicate that the use of the impact factor must be complemented by the cited half-life of the journals, and a composite metric named influence factor is proposed, similar to the R-impact. The h-index is not a good metric anymore because does not correct for authorship inflation. The individual h-index (hi), which takes into account fractional counting of citations, is more reliable than the h-index. An analysis on the use of hi-index with randomly selected 15 Brazilian chemists among the top 500 more productive shows an important effect on the ranking order.
Journal of the Brazilian Chemical Society
The classical alkylation reaction of benzene with isopropyl chloride catalyzed by the species AlC... more The classical alkylation reaction of benzene with isopropyl chloride catalyzed by the species AlCl3 and Al2Cl6 was studied using reliable calculations at M06-2X/def2-TZVPP//X3LYP/def2/SVP level of theory and SMD model for solvent effect. We evaluated the formation of dimers, trimers, tetramers, and pentamers and showed that Al2Cl6 dimers exist in greater proportion, in agreement with experimental observations. The experimental solubility of Al2Cl6 in benzene was also included in the theoretical kinetics analysis. The reaction catalyzed by AlCl3 species presents the highest barrier, in part due to unfavorable dissociation of the Al2Cl6 species. The mechanism via Al2Cl6 catalysis is more effective and even considering its low solubility, the calculated observed ΔG‡ is only 20.6 kcal mol-1, indicating a fast reaction rate. The mechanism involves the formation of the CH3CHCH3+…Al2Cl7− ion pair, which reacts with benzene to form a Wheland intermediate and this carbon-carbon bond formatio...
Journal of Molecular Modeling
RSC Advances, 2016
A reliable theoretical calculation of the free energy profile of a base-catalyzed Knoevenagel rea... more A reliable theoretical calculation of the free energy profile of a base-catalyzed Knoevenagel reaction shows that hydroxide ion elimination step is rate determining.
Journal of the Chemical Society-Perkin Transactions 2, 2000
ABSTRACT
Química Nova, 2016
BUILDING THE LIQUID-VAPOUR EQUILIBRIUM CURVE THROUGH A CUBIC EQUATION OF STATE: USE OF EXCEL FOR ... more BUILDING THE LIQUID-VAPOUR EQUILIBRIUM CURVE THROUGH A CUBIC EQUATION OF STATE: USE OF EXCEL FOR TEACHING PHYSICAL-CHEMISTRY. Cubic equations of state are able to predict the liquid-vapour coexistence curve of volatile substances. However, this property is rarely used to teach Physical Chemistry because solving the resulting equations require numerical technics and many mathematical operations. In this report was shown how the interactive method for finding the root of an equation can be applied with the Excel to determine the vapour pressure of the liquid, as well as the molar volumes of the gas and liquid phases. The generated points was used to build the curves of phase transition in the P × V and P × T graphics.
Theoretical Chemistry Accounts, 2014
ABSTRACT
Physical Chemistry Chemical Physics
Accurate calculation of the solvation free energy of single ions remains an important goal, invol... more Accurate calculation of the solvation free energy of single ions remains an important goal, involving the development in the dielectric continuum solvation models, statistical mechanics with explicit solvent and hybrid...
Asian Journal of Organic Chemistry
Arkivoc
Theoretical modeling of the formation imines in aqueous medium from the reaction of amines with a... more Theoretical modeling of the formation imines in aqueous medium from the reaction of amines with aldehydes is difficult due to formation of charged species, zwitterions, acid-base equilibria and a substantial solvent effect. In this work, a model reaction of methylamine with acetaldehyde was investigated involving neutral and ionic pathways, influence of the pH and different approaches for treating the solvent effect. We have found a mechanism able to explain the fast kinetics of this system, involving the zwitterion formation followed by its isomerization to the carbinolamine and an easy iminium ion formation via an ionic elimination mechanism.
Journal of the Brazilian Chemical Society, 2016
In the past seven years, the SMD (Solvent Model Density) method has been widely used by computati... more In the past seven years, the SMD (Solvent Model Density) method has been widely used by computational chemists. Thus, assessment on the reliability of this model for modeling chemical process in solution is worthwhile. In this report, it was investigated six anion-molecule nucleophilic substitution reactions in methanol and dipolar aprotic solvents. Geometry optimizations have been done at SMD/X3LYP level and single point energy calculations at CCSD(T)/TZVPP + diff level. Our results have indicated that the SMD model is not adequate for dipolar aprotic solvents, with a root of mean squared (RMS) error of 5.6 kcal mol-1 , while the Polarizable Continuum Model (PCM) method with the Pliego and Riveros atomic cavities has led to RMS error of only 3.2 kcal mol-1. For methanol solvent, the SMD method has a RMS error of 3.0 kcal mol-1. The classical protic to dipolar aprotic solvent rate acceleration effect was not predicted by the SMD model for the tested systems.
Química Nova
FORMATION OF AZEOTROPES FROM THE STANDPOINT OF SOLVATION THERMODYNAMICS. The formation of azeotro... more FORMATION OF AZEOTROPES FROM THE STANDPOINT OF SOLVATION THERMODYNAMICS. The formation of azeotropes is related to the deviation of the ideality of liquid mixtures. This deviation is expressed by the activity coefficient of each component. However, the physical origin of this behavior is not well quantified in terms of molecular interactions. In this work, a regular solution model was used, relating the β parameter to the solvation free energy of pure liquids in themselves and in the other component. A mathematical expression was derived that indicates when an azeotrope is formed. This equation shows that the greater the difference in vapour pressure between components, the greater the solvation difference of each liquid in itself and in the other component is needed to form the azeotrope. A set of 10 mixtures were randomly chosen and investigated as a test, and the equation worked in all cases.
Computational and Theoretical Chemistry
Organic & Biomolecular Chemistry
A general view of the medium effects on ionic reactions involves the solvent effect, ion pairing,... more A general view of the medium effects on ionic reactions involves the solvent effect, ion pairing, formation of aggregates and structured environment.
Molecular Systems Design & Engineering
A new macrocycle combining thiourea and crown ether groups is able to solubilize KF and promote f... more A new macrocycle combining thiourea and crown ether groups is able to solubilize KF and promote fluorination via stabilization of the SN2 transition state via four hydrogen bonds.
Physical Chemistry Chemical Physics
Amino-thiourea organocatalysis is an important catalytic process for enantioselective conjugate a... more Amino-thiourea organocatalysis is an important catalytic process for enantioselective conjugate addition reactions.
Theoretical Chemistry Accounts
Anion-molecule reactions have a substantial solvent effect, which decreases with the solvent pola... more Anion-molecule reactions have a substantial solvent effect, which decreases with the solvent polarity. However, less solvation leads to the formation of ion pairs and higher aggregates that are usually less reactive. Consequently, theoretical determination of the best solvent for the reaction needs to consider all the species in equilibrium. In this report, we have investigated the wide range of solvent polarity in the S N Ar reaction of the tetramethylammonium fluoride (TMAF) with 2-bromobenzonitrile, as well as the formation of ion pairs, dimers and tetramers using molecular dynamics and density functional calculations with continuum solvation. Five solvents were considered: methanol, dimethylformamide, pyridine, tetrahydrofuran and benzene. The TMAF exists predominantly as free ions in methanol, as ion pairs in dimethylformamide and pyridine, and as tetramers in tetrahydrofuran and benzene. The reaction takes place through free ions in methanol, ion pairs in dimethylformamide, pyridine and tetrahydrofuran, and via dimer in benzene. The calculations suggest that dimethylformamide and pyridine are the best solvents for this reaction.
Química Nova
Finding the most efficient solvent for a chemical reaction can demand costly experimental procedu... more Finding the most efficient solvent for a chemical reaction can demand costly experimental procedure and the screening is usually limited to few solvents. The use of theoretical methods could accelerate the search for the best solvent, able to promote most effective kinetics and thermodynamics of a reaction. In this work, it was proposed an automated procedure that calculates the solvent effect for a chemical reaction using all the 179 solvents available in SMD (solvation model density). The reaction of 2-bromoacetophenone with pyridine was used as a test. The SMD model correctly predicts the reactivity trends for five solvents, which experimental data are available. We have found that sulfolane, a less usual solvent, is the best one for this reaction. The present study points out that computational screening of large set of solvents using the SMD model is a viable approach and could be useful for chemical reactions optimization.
International Journal of Quantum Chemistry
Journal of Molecular Modeling