Intramolecular pi-pi stacking interactions in 2-substituted N,N-dibenzylaziridinium ions and their regioselectivity in nucleophilic ring-opening reactions

The ring opening of 2-substituted N,N-dibenzylaziridinium ions by bromide is known to occur exclusively at the Substituted aziridine carbon atom via ail S(N)2 mechanism, whereas the opposite regioselectivity has been observed as the main pathway for ring opening by fluoride. Similarly, the hydride-induced ring opening of 2-substituted N,N-dibenzylaziridinium ions has been shown to take place solely at the less hindered position. To gain insight into the main factors causing this difference in regioselectivity, a thorough and detailed computational analysis was performed on the hydride- and halide-induced ring openings of l-benzyl-l-(alpha-(R)-methylbenzyl)-2(S)-(phenoxymethyl)aziridinium bromide. Intramolecular pi-pi stacking interactions in the aziridinium System were investigated at a range of levels that enable a proper description of dispersive interactions; a T-stacking conformer was found to be the most stable. Ring-opening mechanisms were investigated with it variety of DFT and high level ab initio methods to test the robustness of the energetics along the pathway in terms of the electronic level of theory. The necessity to utilize explicit solvent molecules to solvate halide ions was clearly shown; the potential energy surfaces for nonsolvated and solvated cases differed dramatically. It was shown that in the presence of a kinetically viable route, product distribution will be dictated by the energetically preferred pathway; this was observed in the case of hard nucleophiles (both hydride donors and fluoride). However, For the highly polarizable soft nucleophile (bromide), it was shown that in the absence of a large energy difference between transition states leading to competing pathways, the formation of the thermodynamic product is likely to be the driving force. Distortion/interaction analysis on the transition states has shown a considerable difference in interaction energies for the solvated fluoride case, pointing to the fact that sterics plays a major role in the outcome, whereas for the bromide this difference was insignificant, suggesting bromide is less influenced by the difference in sterics

Competitive pathways for peptide deamidation

Asparagine (Asn) residues spontaneously – yet non-enzymatically – deamidate to form aspartate under physiological conditions, causing time-dependent changes in the conformation of proteins, limiting their lifetime [1]. The 'molecular clocks' hypothesis [2], suggests that deamidation is a biological molecular timing mechanism that could be set to any desired time interval by genetic control of the protein structure and the immediate environment of the Asn residue. The fact that deamidation occurs over a wide range of biologically relevant time intervals suggests that different mechanisms may be at play. To date deamidation is believed to occur over a succinimide-mediated pathway [3]. A novel route leading to the succinimide intermediate via tautomerization of the Asn side chain amide functionality was recently proposed [4,5]. The current study introduces a new 'competing' route for the deamidation of asparagine residues. The aim is to comparatively analyze the feasibility of this new mechanism against the traditional succinimide route, taking into account the catalytic effect of the solvent environment. For this purpose, QM dynamics and meta-dynamics calculations were performed on a model peptide placed in a periodic water box. These results will identify the lowest energy pathway for asparagine deamidation and will serve as a stepping stone for QM/MM calculations of Asn deamidation in proteins

A theoretical study of the mechanism of the desymmetrization of cyclic meso-anhydrides by chiral amino alcohols

The alcoholysis of cyclic meso-anhydrides catalyzed by β-amino alcohols has been investigated with DFT quantum mechanics to determine the mechanism of this reaction. Both nucleophilic catalysis and general base catalysis pathways are explored for methanol-induced ring opening of an anhydride catalyzed by a chiral amino alcohol. The nucleophilic pathway involves a late transition state with a high energy barrier. In this mechanism, methanolysis is expected to take place following the amine-induced ring opening of the anhydride. In the base-catalyzed mechanism, methanol attack on one carbonyl group of the meso-anhydride is assisted by the β-amino alcohol; the amine functionality abstracts the methanol proton. The chiral amino alcohol also catalyzes the reaction by stabilizing the oxyanion that forms upon ring opening of the anhydride by hydrogen bonding with its alcoholic moiety. Both stepwise and concerted pathways have been studied for the general base catalysis route. Transition structures for both are found to be lower in energy than in the nucleophilic mechanism. Overall this study has shed light on the mechanism of the β-amino alcohol-catalyzed alcoholysis of cyclic meso-anhydrides, showing that the nucleophilic pathway is approximately 100 kJ mol−1 higher in energy than the general base pathwa

Reactivity of three-membered heterocyclic rings with respect to sodium methoxide

Aziridines can be ‘activated’ or ‘non-activated’, depending on whether their N-substituent is an electron-withdrawing group or an electron-donating group, respectively. Activated aziridines are much more susceptible to ring opening than non-activated aziridines and epoxides are even more reactive. The difference in reactivity between activated 2-(bromomethyl)-1-tosylaziridines, non-activated 1-benzyl-2-(bromomethyl)aziridines and epibromohydrins with respect to sodium methoxide was comparatively analysed by means of DFT calculations, such as BMK, MPW1K and MPWB95 [1]. Nucleophilic substitution reactions are known to be influenced by the solvent environment. Therefore, the gas-phase results were extended towards a discrete solvent approach. The solvent effect was taken into account by inspecting the convergence behaviour of the energy of solvation in terms of a systematically increasing number of solvent molecules. To model each of the reactive profiles of the various substrates, a supermolecule model was used with five explicit methanol molecules. Solvation has significantly changed the landscape of the energy profiles, which nicely shows the necessity of taking into account explicit solvation molecules to obtain the correct reaction profiles. The barriers for direct displacement of bromide by methoxide in methanol are comparable for all three heterocyclic species under study. However, ring opening is only feasible for the epoxide and the activated aziridine and not for the non-activated aziridine

Elucidation of the acetamide hydrolysis mechanism using QM metadynamics simulations

The reaction mechanism for the hydrolysis of amide bonds is a much debated topic in literature. This is not surprising when considering the variety of biologically significant domains in which this reaction is of interest, ranging from peptide bonds to protein side chain degradation. For instance, asparagine (Asn) and glutamine (Gln) residues are known to undergo spontaneous nonenzymatic deamidation in water to form aspartic acid and glutamic acid residues under physiological conditions. Deamidation could be the result of a hydrolysis reaction, either via a concerted or a stepwise mechanism. Gas phase calculations have shown that explicit water molecules play an important role in this reaction, but to date, no simulations of hydrolysis pathways using a periodic water model have been performed. In this work, we perform quantum mechanical metadynamics simulations on the hydrolysis of acetamide as a model compound for Asn or Gln. The periodic simulation cell consists of one acetamide molecule and 90 water molecules in a cubic 15 Å box. From all previously suggested pathways and a new, alternative route, the most competitive pathway can be identified. These results give a clearer insight in deamidation processes proteins and polypeptides and show that an adequate description of the natural surroundings the active species is necessary for obtaining a realistic image of biological processes