Kinetic Study on SNAr Reaction of 1-(Y-Substituted-phenoxy)-2,4-dinitrobenzenes with Cyclic Secondary Amines in Acetonitrile: Evidence for Cyclic Transition-State Structure

Kinetics and Reaction Mechanism of Biothiols Involved in SNAr Reactions: An Experimental Study

Few kinetic parameters, or reaction rates, are known up to date in detail about 1-chloro and 1-fluoro-2,4-dinitrobenzene (ClDNB and FDNB, respectively) with a series of biothiols in aqueous media. These biological nucleophiles with thiol groups have been widely used as a reference in nucleophile reactivity assays due to their prevalence and cellular abundance. The main aim of this study was to elucidate the reaction mechanism based on Brönsted-type plots and reactivity patterns of the electrophile/nucleophile pairs. A complete kinetic study was performed in terms of the comparison of Brönsted-type slope parameters (β_nuc) for the reactions and was used for assigning the mechanism and the rate-determining step associated with the reaction route. A mass spectrometry analysis demonstrated that the nucleophilic center of the biothiols is the -SH group and there is only one kinetic product. The kinetic study suggests that the reaction mechanism might be the borderline between concerted and stepwise pathways. An amine–enol equilibrium for the most reactive nucleophiles appears to be the main determining factor controlling the nucleophilic attack in the nucleophilic aromatic substitution reactions investigated, highlighting the anionic form for these nucleophiles. This amine–enol equilibrium involves a hydrogen bond which stabilizes the intermediate species in the reaction pathway. Thus, intramolecular bonds are formed and enhance the nucleophilic strength through the contribution of the solvent surrounding the electrophile/nucleophile pairs. Finally, we highlight the importance of the formation of electrophile/nucleophile adducts that could modify structures and/or functions of biological systems with potential toxic effects. Therefore, it is essential to know all these kinetic and reactivity patterns and their incidence on other studies.

Kinetic Study on Pyridinolysis of Aryl Benzenesulfonates: Factors Governing Regioselectivity and Reaction Mechanism

A kinetic study is reported for reactions of 2,4-dinitrophenyl X-substituted-benzenesulfonates (1a-1f) and Y-substituted-phenyl benzenesulfonates (2a-2f) with Z-substituted-pyridines. The reactions proceed through S‒O and C‒O bond scissions competitively. The Yukawa-Tsuno plot for the reactions of 1a-1f with 4-oxypyridine (S‒O bond fission) exhibits an excellent linearity. The Brønsted-type plot for the reactions of 2,4-dinitrophenyl benzenesulfonate (1d) with pyridines (S‒O bond fission) is also linear with βnuc = 0.62. The Brønsted-type plot for the reactions of 2a-2f with 4-oxypyridines (S‒O bond fission) is linear with βlg= ‒1.17. Thus, the reactions have been concluded to proceed through a concerted mechanism, in which leaving-group expulsion is significantly more advanced than bond formation between the electrophilic center and nucleophile at the transition state. The Hammett plot for the reactions of 1a-1f with 4-oxypyridine (C‒O bond fission) exhibits scattered points with ρX= 0.98. The Brønsted-type plot for the reactions of 1d with Z-substituted-pyridines (C‒O bond fission) results in an excellent linear correlation with βnuc = 0.38. Thus, the reactions (C‒O bond fission) have been concluded to proceed through a stepwise mechanism with a Meisenheimer complex, in which expulsion of the leaving group occurs after the rate-determining step. Factors governing regioselectivity and reaction mechanism are discussed.

Evidence of Rate Limiting Proton Transfer in an SNAr Aminolysis in Acetonitrile under Synthetically Relevant Conditions

An early synthetic step in the synthesis of adavosertib, AZD1775, is the S_NAr reaction between 4-fluoronitrobenzene and 1-methylpiperazine in acetonitrile. A simple kinetics-based design of four reaction profiling experiments was used to investigate the kinetics of the reaction for the purpose of building a kinetic model. Fitting of the reaction profile data from two experiments conducted at 70 °C with a different excess of 1-methylpiperazine showed the reaction to follow a third-order rate law with a second-order dependence upon 1-methylpiperazine. This was rationalized in terms of the reaction following a rate-limiting proton transfer mechanism (base catalyzed) in which the progress to product is driven by a proton transfer involving a second molecule of 1-methylpiperazine. The experimentally determined entropy of activation of -180 J K^-1 is consistent with this mechanism. The formation of a low level impurity was found to be due to the presence of traces of piperazine in the 1-methylpiperazine, which was shown to react approximately 15 times faster than 1-methylpiperazine at 70 °C. The rate constants for the 1-methylpiperazine catalyzed reaction of piperazine, 1-methylpiperazine, and the piperazine derived impurity were found to correlate in a Brønsted type analysis with the pK_a's (acetonitrile) of the amine nucleophile.

Nucleophilicity Prediction via Multivariate Linear Regression Analysis

The concept of nucleophilicity is at the basis of most transformations in chemistry. Understanding and predicting the relative reactivity of different nucleophiles is therefore of paramount importance. Mayr’s nucleophilicity scale likely represents the most complete collection of reactivity data, which currently includes over 1200 nucleophiles. Several attempts have been made to theoretically predict Mayr’s nucleophilicity parameters N based on calculation of molecular properties, but a general model accounting for different classes of nucleophiles could not be obtained so far. We herein show that multivariate linear regression analysis is a suitable tool for obtaining a simple model predicting N for virtually any class of nucleophiles in different solvents for a set of 341 data points. The key descriptors of the model were found to account for the proton affinity, solvation energies, and sterics.

Experimental Analyses Emphasize the Stability of the Meisenheimer Complex in a SNAr Reaction Toward Trends in Reaction Pathways

The mechanism of S_NAr reactions between 2-chloro-5-nitropyrimidine with primary and secondary alicyclic amines, respectively, have been studied by kinetic measurements. The kinetic data obtained in aqueous media opens a controversial discussion based on Brönsted-type plots analysis. The first approach based on the kinetic data reveals a non-catalyzed pathway. Then, the subtlety of the mathematical treatment of the kinetic data is discussed over a concerted or stepwise mechanism, respectively.

Unexpected medium effect on the mechanism for aminolysis of aryl phenyl carbonates in acetonitrile and H2O: transition-state structure in the catalytic pathway

Upward curvature in the kinetic plots of pseudo first-order rate constants (kobsd) vs. [amine] for the aminolysis of aryl phenyl carbonates (5a–5j) in MeCN demonstrates that these reactions proceed via a zwitterionic tetrahedral intermediate (T±) that partitions between catalyzed and uncatalyzed routes to give the products. Yukawa–Tsuno plots for the reactions of 5a–5j with piperidine result in excellent linear correlations with ρY = 4.82 and r = 0.47 for the uncatalyzed reaction versus ρY = 2.21 and r = 0.21 for the catalyzed reaction. Brønsted plots for reactions of 4-(ethoxycarbonyl)-phenyl phenyl carbonate (5f) with a series of cyclic secondary amines exhibit excellent linear correlations with βnuc = 0.87 and 0.58 for the uncatalyzed and catalyzed reactions, respectively. The ΔH‡ and ΔS‡ values are 0.92 kcal/mol and –50.1 cal/mol K, respectively, for the catalyzed reaction of 5f with piperidine. Deuterium kinetic isotope effects found for reactions of 5f with piperidine/deuterated piperidine are 0.84 (uncatalyzed) and 1.42 (catalyzed). Multi-parameter analysis supports a concerted catalytic pathway involving a six-membered cyclic transition state rather than a traditionally accepted stepwise pathway with an anionic intermediate. The current unexpected results, where T± is the essential central intermediate in this aminolysis, contrast with previous calculation studies that deemed T± unstable in gas phase or MeCN.

Medium effect (water versus MeCN) on reactivity and reaction pathways for the SNAr reaction of 1-aryloxy-2,4-dinitrobenzenes with cyclic secondary amines

A kinetic study on SNAr reactions of 1-aryloxy-2,4-dinitrobenzenes (1a–1h) with a series of cyclic secondary amines in 80 mol% water – 20 mol% DMSO at 25.0 ± 0.1 °C is reported. The plots of kobsd versus amine concentration curve upward except for the reactions of substrates possessing a strong electron-withdrawing group in the leaving aryloxide with strongly basic piperidine. The curved plots indicate that the reactions proceed through both uncatalytic and catalytic routes. Linear Brønsted-type plots have been obtained for the uncatalyzed and catalyzed reactions of 1-(4-nitrophenoxy)-2,4-dinitrobenzene (1a) with βnuc = 0.84 and 0.78, respectively. The Yukawa–Tsuno plot for the uncatalyzed reactions of 1a–1h with piperidine results in an excellent linear correlation with ρ = 1.66 and r = 0.31. In contrast, rate constants for catalyzed reactions are independent of the electronic nature of the substituent in the leaving group. The current SNAr reactions have been proposed to proceed via a zwitterionic intermediate (MC±) that partitions to products through uncatalytic and catalytic routes. The catalyzed reaction from MC± has been concluded to proceed through a concerted mechanism with a six-membered cyclic transition state (TScycl) rather than via a stepwise pathway with a discrete anionic intermediate (MC−), the traditionally accepted mechanism. Medium effects on the reactivity and reaction mechanism are discussed. Particularly, hydrogen bonding of the amines to water precludes formation of kinetically significant dimers found in some aprotic solvents; no explicit role for water in the catalytic transition state is required or proposed. The specific stabilization of the leaving aryloxides substituted with strong electron-withdrawing groups accounts for the lack of the catalytic pathway in these systems (1a–1c) with piperidine nucleophile.

Alkali metal ion catalysis and inhibition in alkaline ethanolysis of O-Y-substituted-phenyl O-phenyl thionocarbonates: contrasting M+ ion effects upon changing electrophilic centre from C=O to C=S

Pseudo-first-order rate constants (kobsd) were measured for nucleophilic substitution reactions of O-Y-substituted-phenyl O-phenyl thionocarbonates (4a–4h) with alkali metal ethoxides (EtOM, M = Li, Na, or K) in anhydrous ethanol at 25.0 ± 0.1 °C. Plots of kobsd vs. [EtOM] exhibited upward curvature for the reaction of O-4-nitrophenyl O-phenyl thionocarbonate (4a) with EtOK in the presence of 18-crown-6-ether (18C6), but showed downward curvature for the reaction with EtOLi, indicating that the reaction is catalyzed by the 18C6-crowned K+ ion, but is inhibited by Li+ ion. The kobsd values were dissected into kEtO− and kEtOM, the second-order rate constant for the reaction with dissociated EtO− and ion-paired EtOM, respectively. The reactivity of EtOM toward 4a increases in the order EtOLi < EtONa < EtO− < EtOK < EtOK/18C6, which is in contrast to that reported previously for the corresponding reaction of 4-nitrophenyl phenyl carbonate (a C=O analogue of 4a), e.g., EtO− ≈ EtOK/18C6 < EtOLi < EtONa < EtOK. The reaction mechanism, including the transition-state model and the origin of the contrasting reactivity patterns found for the reactions of the C=O and C=S compounds, are discussed.

Reactivity and selectivity of the reaction of O,O-diethyl 2,4-dinitrophenyl phosphate and thionophosphate with thiols of low molecular weight

A kinetics control product by sulfhydryl attack of thiols was observed in the reactions of both triesters with Cys and Hcys, followed by an intramolecular amine attack leading to a thermodynamic control product.

The α-effect in the SNAr reaction of 1-(4-nitrophenoxy)-2,4-dinitrobenzene with anionic nucleophiles: effects of solvation and polarizability on the α-effect

A kinetic study on SNAr reactions of 1-(4-nitrophenoxy)-2,4-dinitrobenzene (1a) with various anionic nucleophiles in 80 mol% water – 20 mol% DMSO at 25.0 °C is reported. The Brønsted-type plot for the reaction of 1a with a series of substituted phenoxides and HOO− results in an excellent linear correlation with βnuc = 1.17. However, OH− exhibits dramatic negative deviation from the Brønsted-type plot, while N3−, C6H5S−, and butane-2,3-dione monoximate (Ox−) deviate positively from linearity. HOO− is 680-fold more reactive than OH− but does not exhibit the α-effect. In contrast, Ox− is 166-fold more reactive than isobasic 4-Cl−C6H4O− and exhibits the α-effect. Differential solvation effects have been suggested to be responsible for the α-effect in this study, i.e., Ox− exhibits the α-effect, since it is 5.7 kcal/mol less strongly solvated than 4-Cl−C6H4O− in the reaction medium, while HOO− does not show the α-effect due to a strong requirement for partial desolvation before nucleophilic attack. The highly enhanced reactivity of polarizable N3− and C6H5S− and extremely decreased reactivity of nonpolarizable OH− are in accord with the hard–soft acid and base principle.