DFT studies on the structure and stability of zwitterionic tetrahedral intermediate in the aminolysis of esters

Mechanistic insights into lysine-targeting covalent inhibition through a theoretical study of ester aminolysis

Development of targeted covalent inhibitors in drug design has a broad and important interest and many efforts are currently being made in this direction. Targeted covalent inhibitors have special relevance in oncology due to the possibilities they offer to overcome the problems of acquired resistance. In recent experiments, lysine-targeting has been envisaged for the irreversible inhibition of the heterodimeric lipid kinase phosphoinositide 3-kinase delta (PI3Kδ). Activated esters have been evaluated and shown to be promising inhibitors of this enzyme, but the reaction mechanisms display specificities that are not yet fully understood. In the present work, we have carried out a theoretical study of the aminolysis reaction of model esters in aqueous solution to gain insights into the corresponding biological processes. We have found that phenolic esters bearing electron-withdrawing groups are particularly reactive. The predicted mechanism involves the formation of a tetrahedral zwitterionic intermediate, which dissociates into an alkoxide and a protonated amide, this charge separation being the driving force for the subsequent proton transfer and final product formation. Structure-reactivity relationships are reported and shown to be a useful tool for evaluating potential inhibitor candidates.

Zwitterionic Ring-Opened Oxyphosphonium Species from the Ph3P-I2 Mediated Reactions of Benzo[d]oxazol-2(3H)-ones with Secondary Amines

Instead of the expected substituted 2-aminobenzo[d]oxazoles, relatively stable ring-opened oxyphosphonium betaines were isolated for the first time from the Ph₃P-I₂-mediated reactions of benzo[d]oxazol-2(3H)-ones with acyclic secondary amines. The structure of one of these compounds was unambiguously confirmed by single-crystal X-ray analysis. Thermolysis of the betaines gave rise to 2-dialkylaminobenzoxazoles with concomitant loss of triphenylphosphine oxide, suggesting their possible role as intermediates in an alternative reaction path.

The effect of the electrophilic group on the hierarchy of nucleofuges in the aminolysis reactions of thiol- and dithiocarbonates with secondary alicyclic amines: A kinetic and theoretical study

Thiol- and dithiocarbonates react with amines, forming tetrahedral intermediates and then different product ratios. Theoretical results show that the product ratio depends on the water microsolvation of the electrophilic group in the anionic intermediate.

Experimental and theoretical studies on the nucleofugality ratio in the aminolysis reactions of O-(4-cyanophenyl) O-(3-nitrophenyl) thionocarbonate with amines in aqueous ethanol

The title thionocarbonate reacts with amines to form 4-cyanophenol and 3-nitrophenol in a 1.5 : 1 ratio. Theoretical results show that the products ratio depends on the microsolvation of the water molecules.

Computational Investigation of the Aminolysis of RAFT Macromolecules

This work presents a detailed computational study and kinetic analysis of the aminolysis of dithioates, dithiobenzoates, trithiocarbonates, xanthates, and thiocarbamates, which are frequently used as chain-transfer agents for reversible addition-fragmentation chain-transfer (RAFT) polymerization. Rate coefficients were obtained from ab initio calculations, taking into account a diffusional contribution according to the encounter pair model. A kinetic model was constructed and reveals a reaction mechanism of four elementary steps: (i) formation of a zwitterionic intermediate, (ii) formation of a complex intermediate in which an assisting amine molecule takes over the proton from the zwitterionic intermediate, (iii) breakdown of the complex into a neutral tetrahedral intermediate with release of the assisting amine molecule, and (iv) amine-assisted breakdown of the neutral intermediate to the products. Furthermore, a comparative analysis indicates that the alkanedithioates and dithiobenzoates react the fastest, followed, respectively, by xanthates and trithiocarbonates, which react almost equally fast, and dithiocarbamates, which are not reactive at typical experimentally used conditions.

Concerted amidation of activated esters: reaction path and origins of selectivity in the kinetic resolution of cyclic amines via N-heterocyclic carbenes and hydroxamic acid cocatalyzed acyl transfer

The N-heterocyclic carbene and hydroxamic acid cocatalyzed kinetic resolution of cyclic amines generates enantioenriched amines and amides with selectivity factors up to 127. In this report, a quantum mechanical study of the reaction mechanism indicates that the selectivity-determining aminolysis step occurs via a novel concerted pathway in which the hydroxamic acid plays a key role in directing proton transfer from the incoming amine. This modality was found to be general in amide bond formation from a number of activated esters including those generated from HOBt and HOAt, reagents that are broadly used in peptide coupling. For the kinetic resolution, the proposed model accurately predicts the faster reacting enantiomer. A breakdown of the steric and electronic control elements shows that a gearing effect in the transition state is responsible for the observed selectivity.

Comparison of aminolysis of 2-pyridyl and 4-pyridyl x-substituted benzoates in acetonitrile: evidence for a concerted mechanism involving a cyclic transition state

A kinetic study on reactions of 2-pyridyl X-substituted benzoates (6a-i) with a series of cyclic secondary amines in MeCN is reported. The Hammett plot for the reaction of 6a-i with piperidine consists of two intersecting straight lines while the Yukawa-Tsuno plot exhibits an excellent linear correlation with ρX = 1.28 and r = 0.63, indicating that the nonlinear Hammett plot is not caused by a change in the rate-determining step but rather by resonance stabilization of substrates possessing an electron-donating group (EDG) in the benzoyl moiety. The Brønsted-type plots are linear with βnuc = 0.59 ± 0.02, which is typical of reactions reported to proceed through a concerted mechanism. A cyclic transition state (TS), which forces the reaction to proceed through a concerted mechanism, is proposed. The deuterium kinetic isotope effect of 1.3 ± 0.1 is consistent with the proposed mechanism. Analysis of activation parameters reveals that ΔH(‡) increases linearly as the substituent X changes from an electron-withdrawing group (EWG) to an EDG, while TΔS(‡) remains nearly constant with a large negative value. The constant TΔS(‡) value further supports the proposal that the reaction proceeds through a concerted mechanism with a cyclic TS.

Microsolvated transition state models for improved insight into chemical properties and reaction mechanisms

Over the years, several methods have been developed to effectively represent the chemical behavior of solutes in solvents. The environmental effects arising due to solvation can generally be achieved either through inclusion of discrete solvent molecules or by inscribing into a cavity in a homogeneous and continuum dielectric medium. In both these approaches of computational origin, the perturbations on the solute induced by the surrounding solvent are at the focus of the problem. While the rigor and method of inclusion of solvent effects vary, such solvation models have found widespread applications, as evident from modern chemical literature. A hybrid method, commonly referred to as cluster-continuum model (CCM), brings together the key advantages of discrete and continuum models. In this perspective, we intend to highlight the latent potential of CCM toward obtaining accurate estimates on a number of properties as well as reactions of contemporary significance. The objective has generally been achieved by choosing illustrative examples from the literature, besides expending efforts to bring out the complementary advantages of CCM as compared to continuum or discrete solvation models. The majority of examples emanate from the prevalent applications of CCM to organic reactions, although a handful of interesting organometallic reactions have also been discussed. In addition, increasingly accurate computations of properties like pK(a) and solvation of ions obtained using the CCM protocol are also presented.

Mechanism of the aminolysis of Fischer alkoxy and thiocarbene complexes: a DFT study

B3LYP calculations have been carried out to study the reaction mechanism of the aminolysis of Fischer carbene complexes of the type (CO)(5)Cr=C(XMe)R (X = O and S; R = Me and Ph). We have explored different possible reaction mechanisms either through neutral or zwitterionic intermediates as well as a general base catalysis assisted by an ammonia molecule. Our results show that the most favorable pathway for the aminolysis of Fischer carbene complexes is through a stepwise reaction via a zwitterionic intermediate generated by the initial nucleophilic attack. We have found that the ammonia-catalyzed mechanism entails a significantly lower barrier for the rate-determining step than the uncatalyzed one. At lower pressure gas-phase conditions, the rate-determining step corresponds to the concerted proton transfer and MeXH elimination. Thiocarbene complexes show a higher energy barrier for this rate-determining step due to the lower basicity of the MeS(-) substituent. At higher pressure or in solution, the rate-determining step corresponds to the initial nucleophilic attack. Our results indicate that the transition state of the nucleophilic attack is more advanced and has a higher barrier for alkoxycarbene than thiocarbene complexes due to the stronger pi-donor character of the alkoxy group that reduces the electrophilicity of the attacked carbene atom making the nucleophilic attack more difficult.

Pitfalls in assessing the α-effect: reactions of substituted phenyl methanesulfonates with HOO(-), OH(-), and substituted phenoxides in H(2)O

Toward resolving the current controversy regarding the validity of the α-effect, we have examined the reactions of Y-substituted phenyl methanesulfonates 1a-1l with HOO(-), OH(-), and Z-substituted phenoxides in the gas phase versus solution (H(2)O). Criteria examined in this work are the following: (1) Brønsted-type and Hammett plots for reactions with HOO(-)and OH(-), (2) comparison of β(lg) values reported previously for the reactions of Y-substituted phenyl benzenesulfonates 2a-2k with HOO(-) (β(lg) = -0.73) and OH(-) (β(lg) = -0.55), and for those of 1a-1l with HOO(-) (β(lg) = -0.69) and OH(-) (β(lg) = -1.35), and (3) Brønsted-type plot showing extreme deviation of OH(-) for reactions of 2,4-dintrophenyl methanesulfonate 1a with aryloxides, HOO(-), and OH(-), signifying extreme solvation vs different mechanisms. The results reveal significant pitfalls in assessing the validity of current interpretations of the α-effect. The extreme negative deviation by OH(-) must be due, in part, to the difference in their reaction mechanisms. Thus, the apparent dependence of the α-effect on leaving-group basicity found in this study has no significant meaning due to the difference in operating mechanisms. The current results argue in favor of a further criterion, i.e., a consistency in mechanism for the α-nucleophiles and normal nucleophiles.