Acid-catalyzed nucleophilic additions to carbonyl groups: is the accepted mechanism the rule or an exception?

The transesterification reaction, and in particular the methanolysis of ethyl acetate with sulfuric acid as catalyst, is used as a model reaction to study the acid-catalyzed nucleophilic addition to a carbonyl group. Continuum solvation methods (SMD and IEF-PCM) and the MPWB1K functional are used. The reaction mechanism is studied in methanol and in acetonitrile as solvents. Our results indicate that the acid-catalyzed addition mechanism is stepwise, and the transition state (TS) is a contact ion-pair. The counteranion of the acid catalyst remains in the reaction site playing an important role in the TS of this reaction. Changes in the reaction kinetics and the ionic/nonionic nature of the TS with the ionizing ability of the solvent and the strength of the acid catalyst are explored. Additional calculations at the CBS-Q3 level of theory reinforce the conclusions of this paper. The results obtained allow the generalization of important ideas regarding the mechanism of the nucleophilic addition to carbonyl groups.

Calculating the Aqueous pKa of Phenols: Predictions for Antioxidants and Cannabinoids.

We aim to develop a theoretical methodology for the accurate aqueous pKa prediction of structurally complex phenolic antioxidants and cannabinoids. In this study, five functionals (M06-2X, B3LYP, BHandHLYP, PBE0, and TPSS) and two solvent models (SMD and PCM) were combined with the 6-311++G(d,p) basis set to predict pKa values for twenty structurally simple phenols. None of the direct calculations produced good results. However, the correlations between the calculated Gibbs energy difference of each acid and its conjugate base, ΔGaq(BA)°=ΔGaqA-°-ΔGaq(HA)°, and the experimental aqueous pKa values had superior predictive accuracy, which was also tested relative to an independent set of ten molecules of which six were structurally complex phenols. New correlations were built with twenty-seven phenols (including the phenols with experimental pKa values from the test set), which were used to make predictions. The best correlation equations used the PCM method and produced mean absolute errors of 0.26-0.27 pKa units and R2 values of 0.957-0.960. The average range of predictions for the potential antioxidants (cannabinoids) was 0.15 (0.25) pKa units, which indicates good agreement between our methodologies. The new correlation equations could be used to make pKa predictions for other phenols in water and potentially in other solvents where they might be more soluble.

Complexes of Copper and Iron with Pyridoxamine, Ascorbic Acid, and a Model Amadori Compound: Exploring Pyridoxamine's Secondary Antioxidant Activity.

The thermodynamic stability of 11 complexes of Cu(II) and 26 complexes of Fe(III) is studied, comprising the ligands pyridoxamine (PM), ascorbic acid (ASC), and a model Amadori compound (AMD). In addition, the secondary antioxidant activity of PM is analyzed when chelating both Cu(II) and Fe(III), relative to the rate constant of the first step of the Haber-Weiss cycle, in the presence of the superoxide radical anion (O2•-) or ascorbate (ASC-). Calculations are performed at the M05(SMD)/6-311+G(d,p) level of theory. The aqueous environment is modeled by making use of the SMD solvation method in all calculations. This level of theory accurately reproduces the experimental data available. When put in perspective with the stability of various complexes of aminoguanidine (AG) (which we have previously studied), the following stability trends can be found for the Cu(II) and Fe(III) complexes, respectively: ASC < AG < AMD < PM and AG < ASC < AMD < PM. The most stable complex of Cu(II) with PM (with two bidentate ligands) presents a ΔGf0 value of -35.8 kcal/mol, whereas the Fe(III) complex with the highest stability (with three bidentate ligands) possesses a ΔGf0 of -58.9 kcal/mol. These complexes can significantly reduce the rate constant of the first step of the Haber-Weiss cycle with both O2•- and ASC-. In the case of the copper-containing reaction, the rates are reduced up to 9.70 × 103 and 4.09 × 1013 times, respectively. With iron, the rates become 1.78 × 103 and 4.45 × 1015 times smaller, respectively. Thus, PM presents significant secondary antioxidant activity since it is able to inhibit the production of ·OH radicals. This work concludes a series of studies on secondary antioxidant activity and allows potentially new glycation inhibitors to be investigated and compared relative to both PM and AG.

Thermodynamic stability of neutral and anionic PFOS: a gas-phase, n-octanol, and water theoretical study.

The thermodynamic stability of the 89 isomers of the eight-carbon-atom compound perfluorooctane sulfonate (PFOS) in their neutral and anionic forms has been studied in the gas phase, n-octanol, and water using density functional theory (B3LYP/6-311+G(d,p)). The gas-phase calculations are compared with previous semiempirical and partial ab initio studies; the calculations in water and n-octanol are reported for the first time. The results obtained indicate that the thermodynamic stability assessment of this family of persistent organic pollutants is independent of the environment and type of species (neutral or anionic) considered and that it is important to consider other PFOSs outside of the 83-89 set, which is the most frequently studied.

Theoretical Study of the Iron Complexes with Aminoguanidine: Investigating Secondary Antioxidant Activity.

A thorough analysis of the thermodynamic stability of various complexes of aminoguanidine (AG) with Fe(III) at a physiological pH is presented. Moreover, the secondary antioxidant activity of AG is studied with respect to its kinetic role in the Fe(III) reduction to Fe(II) when reacting with the superoxide radical anion or ascorbate. Calculations are performed at the M05(SMD)/6-311+G(d,p) level of theory. Solvent effects (water) are taken into account in both geometry optimizations and frequency calculations employing the SMD solvation method. Even though the results of this study show that AG can form an extensive number of stable complexes with Fe(III), none of these can reduce the rate constant of the initial step of the Haber-Weiss cycle when the reducing agent is O2•-. However, when the reductant is the ascorbate anion, AG is capable of reducing the rate constant of this reaction significantly, to the point of inhibiting the production of •OH radicals. In fact, the most stable complex of Fe(III) with AG, having a ∆Gf° of -37.9 kcal/mol, can reduce the rate constant of this reaction by 7.9 × 105 times. Thus, AG possesses secondary antioxidant activity relative to the Fe(III)/Fe(II) reduction with ascorbate, but not with O2•-. Similar results have also been found for AG relative to the Cu(II)/Cu(I) reduction, in agreement with experimental results.

Theoretical Study of the Copper Complexes with Aminoguanidine: Investigating Secondary Antioxidant Activity.

A systematic study of the thermodynamic stability of various Cu(II) complexes with aminoguanidine (AG) is performed, together with the study of its secondary antioxidant activity. Calculations have been carried out at the M05(SMD)/6-311+G(d,p) level of theory using water as the solvent. The results obtained indicate that AG is capable of forming a wide array of stable coordination compounds with Cu(II) under physiological pH conditions, and it possesses some degree of secondary antioxidant activity when coordinating to copper. The most thermodynamically stable complex can slow down 2.8 times the first step of the Haber-Weiss cycle (from 7.71 × 109 to 2.80 × 109 M-1 s-1) and slightly reduce the potential damage that the formation of •OH radicals can cause. The results of this research add to previous knowledge on this molecule, which could be used as a potential glycation inhibitor.

Theoretical Study of the Iron Complexes with Lipoic and Dihydrolipoic Acids: Exploring Secondary Antioxidant Activity.

The thermodynamic stability of twenty-nine Fe(III) complexes with various deprotonated forms of lipoic (LA) and dihydrolipoic (DHLA) acids, with coordination numbers 4, 5 and 6, is studied at the M06(SMD)/6-31++G(d,p) level of theory in water under physiological pH conditions at 298.15 K. Even though the complexes with LA- are more stable than those with DHLA-, the most thermodynamically stable Fe(III) complexes involve DHLA2-. The twenty-four exergonic complexes are used to evaluate the secondary antioxidant activity of DHLA and LA relative to the Fe(III)/Fe(II) reduction by O2•- and ascorbate. Rate constants for the single-electron transfer (SET) reactions are calculated. The thermodynamic stability of the Fe(III) complexes does not fully correlate with the rate constant of their SET reactions, but more exergonic complexes usually exhibit smaller SET rate constants. Some Cu(II) complexes and their reduction to Cu(I) are also studied at the same level of theory for comparison. The Fe(III) complexes appear to be more stable than their Cu(II) counterparts. Relative to the Fe(III)/Fe(II) reduction with ascorbate, DHLA can fully inhibit the formation of •OH radicals, but not by reaction with O2•-. Relative to the Cu(II)/Cu(I) reduction with ascorbate, the effects of DHLA are moderate/high, and with O2•- they are minor. LA has minor to negligible inhibition effects in all the cases considered.

Copolymerization of CHO/CO2 catalyzed by a series of aluminum amino-phenolate complexes and insights into structure-activity relationships.

Two series of monometallic aluminum complexes were prepared and characterized by elemental analyses, 1H and 13C{1H} NMR spectroscopy, and X-ray crystallography: Al[L]X, where [L] = dimethylaminoethylamino-N,N-bis(2-methylene-4,6-tert-butylphenolate) and X = Cl, OEt, and Al[L]2Cl, where [L] = 6-{[(2R,6R)-2,6-dimethyl-4-morpholino]methylene}-2,4-bis(tert-butyl)phenolate or 6-(piperidinomethylene)-2-(tert-butyl)-4-(methyl)phenolate. All the complexes, including the previously reported morpholinyl complex Al[L]Cl, where [L] = 4-(2-aminoethyl)morpholinylamino-N,N-bis(2-methylene-4,6-tert-butylphenolate), were tested as catalysts for copolymerization of cyclohexene oxide and CO2 in the presence and absence of PPNCl. When coupled with 1 equiv. PPNCl, the complexes exhibit similar activities and the best selectivity for poly(cyclohexenecarbonate) vs. the cyclic product, cyclohexene carbonate, was obtained with the morpholinyl complex (ca. 90%) whereas significantly lower selectivities (<1-63%) were obtained with the other complexes. Preliminary DFT calculations investigating this difference in selectivity were carried out by analyzing the aluminum partial atomic charges in the Al-carbonate intermediates.

The Baeyer-Villiger reaction: solvent effects on reaction mechanisms.

This study focuses on the Baeyer-Villiger reaction of propanone and performic acid, with formic acid as catalyst. Continuum solvation methods (EIF-PCM and CPCM) and two density functionals (B3LYP and MPWB1K) are used to study solvent effects on two types of reaction mechanisms: concerted non-ionic and stepwise ionic. The ionic mechanism is the one found in most organic chemistry textbooks; it begins with the protonation of the ketone by the acid catalyst, even though this reaction normally takes place in non-polar solvents such as dichloromethane. Our calculations show that the concerted non-ionic pathway, which is the least energetic in non-polar solvents such as dichloromethane, becomes more energetic the more polar the solvent. After investigating a variety of non-ionic and ionic pathways in water, it is found that the addition step seems to be ionic but the migration step, which is rate-determining, is uncatalyzed, non-ionic and fully concerted. These results confirm the experimental findings in solvents of low to medium polarity that the rate constant of the reaction decreases as the solvent polarity increases. Moreover, we find that contrary to what is commonly accepted, in the addition and migration ionic steps the deprotonation of the ionic species occurs in a concerted manner with the other chemical events taking place.

Theoretical Study of the Reactivity and Selectivity of Various Free Radicals with Cysteine Residues.

Radicals in biochemical environments can lead to protein damage. Theoretical studies can help us to understand the observed radical selectivity. In this work, the kinetics and thermodynamics of the hydrogen-transfer (HT) and single-electron transfer (SET) reactions between a cysteine derivative and 17 free radicals of biological significance have been theoretically investigated in aqueous and lipid media. With the exception of the reaction with •OCCl3, all SET reactions in aqueous medium have rate constants in the diffusion-limited regime. The γ site of cysteine was found to be the most reactive for the HT reactions with all the radicals, with rate constants in the diffusion limit for •OH, •OCHCl2, and •OCCl3. The HT reactions from the α and γ positions have very similar ΔG° values and even though the ß position is the least thermodynamically favored, when the HT from ß is exergonic it is a more reactive site than α. The results obtained confirm that the Bell-Evans-Polanyi principle does not apply to the reactions between amino acid residues and free radicals and that reactivity comparisons demand proper kinetic calculations.

Computational determination of aqueous pKa values of protonated benzimidazoles (Part 2).

Our aim is to develop an effective computational procedure for predicting the aqueous acid equilibrium constants of protonated benzimidazoles at 298.15 K. The experimental determination of these values, apart from been laborious, is a challenge because of the low water solubility of these compounds. Using a variety of descriptors, quantitative structure-property relationships (QSPR) are explored between the experimental aqueous pKa values of a group of fifteen benzimidazoles and descriptors calculated at the B3LYP/6-31+G(d,p) level of theory. Solvent effects are taken into account with the PCM solvation model through both single-point energy calculations (PCM(sp)), and in the geometry optimizations and frequency calculations (PCM(opt)). Descriptors considered are the Gibbs free-energy change of the acid equilibrium in water, the charges on the acidic hydrogen, and on the basic nitrogen, several orbital energies of the protonated and neutral species, and the volume of the solvent cavity. Multiple linear regressions are used to correlate descriptors to the experimental pKa values. Several QSPR equations reproduce the experimental data more accurately, and show stronger correlations than previously attempted methodologies. The predictive capabilities of the QSPR methodologies are tested with four compounds that were not included in the set of benzimidazoles initially investigated. In addition, a correlation between experimental pKa values in water and in a 50% ethanol-water solution is used to estimate aqueous pKa values.

Computational determination of aqueous pKa values of protonated benzimidazoles (part 1).

Benzimidazoles are the organic compounds investigated in this work. The experimental determination of the pKa values of protonated benzimidazoles in water is a challenge because of their low solubility. In addition, some derivatives are involved in tautomeric equilibria which increase the complexity of the theoretical pKa determinations. In the present study, different approaches are considered to develop a methodology for the accurate prediction of aqueous pKa values of protonated benzimidazoles at 298.15 K. We have considered different reaction schemes for approximating the acid dissociation equilibrium; two distinct equations are used for the calculation of pKa values, and a number of levels of theory and empirical corrections are applied in the process of working toward this aim. The best correlations between the experimental and calculated data are obtained at the B3LYP/6-31+G(d,p)-PCM(opt) level of theory. The predictive capabilities of the methodologies attempted are tested with two compounds that were not included in the set of benzimidazoles initially investigated. The direct calculations differ significantly from the expected values, but the pKa values calculated using the correlation equations are very similar and in reasonable agreement with the expected pKa values.

Interaction of brassinolide with essential amino acid residues: a theoretical approach.

The interaction of the most active natural brassinosteroid, brassinolide, with the twenty natural amino acids is studied applying the multiple minima hypersurface method to model the molecular interactions explicitly. The resulting thermodynamic data gives useful information about the amino acids with the greatest association for brassinolide and the stabilities of such complexes. Density functional theory (DFT) optimizations were further carried out to test the performance of semiempirical calculations. Additional calculations with a more accurate DFT method were performed to explore the formation of this type of molecular complexes. The semiempirical geometries and stability order of these complexes are in good agreement with the DFT calculations. Each group of amino acids possesses a preferential zone of interaction with brassinolide, forming the polar-charged amino acids the most stable complexes. This study could contribute to future investigations of the interaction of brassinosteroids with the receptor protein in plants.

The mechanism of the Baeyer-Villiger rearrangement: quantum chemistry and TST study supported by experimental kinetic data.

The mechanism of the Baeyer-Villiger rearrangement is modelled for the reaction of propanone with trifluoroperacetic acid, catalyzed by trifluoroacetic acid in dichloromethane, using three DFT methods (B3LYP, BH&HLYP and MPWB1K) and MP2. These results are refined and used to calculate the overall reaction rate coefficient using conventional Transition State Theory. The excellent agreement between the calculated (1.00 x 10(-3) L mol(-1) s(-1)) and the experimental (1.8 x 10(-3) L mol(-1) s(-1)) rate coefficients at the MPWB1K level strongly supports the mechanism recently proposed by our group. This DFT method is then used to study the mechanism of a larger system: cyclohexanone + trifluoroperacetic acid, for which a very good agreement between the calculated and the experimental rate coefficients is also found (1.37 and 0.32 L mol(-1) s(-1), respectively). The modelled mechanism is not ionic but neutral, and consists of two concerted steps. The first one is strongly catalyzed while the second one, the migration step, seems not to be catalyzed for the systems under study. The results of this work could be of interest for understanding other reactions in non-polar solvents for which ionic mechanisms have been assumed.