Quantum chemical calculations are reported to provide new insights on plausible mechanisms leading to the deamidation of asparagine residues in proteins and peptides. Direct hydrolysis to aspartic acid and several succinimide-mediated mechanisms have been described. The catalytic effect of water molecules has been explicitly analyzed. Calculations have been carried out at the density functional level (B3LYP/6-31+G**). Comparisons of free energy profiles show that the most favorable reaction mechanism goes through formation of a succinimide intermediate and involves tautomerization of the asparagine amide to the corresponding imidic acid as the initial reaction step. Another striking result is that direct water-assisted hydrolysis is competitive with the succinimide-mediated deamidation routes even in the absence of acid or base catalysis. The rate-determining step for the formation of the succinimide intermediate is cyclization, regardless of the mechanism. The rate-determining step for the complete deamidation is the hydrolysis of the succinimide intermediate. These results allow clarification of some well-known facts, such as the isolation of succinimide or the absence of iso-Asp among the reaction products observed in some experiments.
This study deals with modeling the propagation and the chain transfer reactions in the free radical polymerization of ethylene, methyl methacrylate (MMA), and acrylamide (AM). The chain transfer agents modeled in the free radical polymerization of ethylene are the experimentally widely used species such as ethylene, methane, ethane, propane, trimethylamine, dimethylamine, chloroform, and carbon tetrachloride. The role of 4-X-thiophenols as chain transfer agents in the polymerization of MMA and AM has been investigated. Geometry optimizations have been carried out with the B3LYP/6-31+G(d) methodology. Reaction rate constants are calculated via the standard transition-state theory with the B3LYP/6-311+G(3df,2p)//B3LYP/6-31+G(d), MPWB1K/6-311+G(3df,2p)//B3LYP/6-31+G(d), and M05-2X/6-311+G(3df,2p)//B3LYP/6-31+G(d) methodologies, which reproduce qualitatively the experimental trends for the chain transfer rate constants. The usage of simple continuum models with the MPWB1K/6-311+G(3df,2p)//B3LYP/6-31+G(d) methodology for the solvation energies has slightly improved the accurate prediction of the chain transfer constants. Polar interactions highly influence the barrier heights for chain transfer reactions in the FRP of ethylene, MMA, and AM. Calculated chain transfer rate constants in the FRP of MMA and AM correlate quite well with the Hammett constants.
Deamidation of proteins occurs spontaneously under physiological conditions. Asparaginyl (Asn) residues may deamidate into aspartyl (Asp) residues, causing a change in both the charge and the conformation of peptides. It has been previously proposed by Capasso et al. that deamidation of relatively unrestrained Asn residues proceeds through a succinimide intermediate. This mechanism has been modeled by Konuklar et al. and the rate determining step for the deamidation process in neutral media has been shown to be the cyclization step leading to the succinimide intermediate. In the present study, possible water-assisted mechanisms, for both concerted and stepwise succinimide formation, were computationally explored using the B3LYP method with 6-31+G* basis set. Single point solvent calculations were carried out in water, by means of integral equation formalism-polarizable continuum model (IEF-PCM) at the B3LYP/6-31++G* level of theory. A novel route leading to the succinimide intermediate via tautomerization of the Asn side chain amide functionality has been proposed. The energetics of these pathways have been subject to a comparative study to identify the most probable mechanism for the deamidation of peptides in solution.
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