Promotion Energy Analysis Predicts Reaction Modes: Nucleophilic and Electrophilic Aromatic Substitution Reactions

A mechanistic continuum of nucleophilic aromatic substitution reactions with azole nucleophiles

Nucleophilic aromatic substitution (SNAr) is a broadly used method for generating structural complexity in pharmaceuticals. Although SNAr reactions were long assumed to be stepwise, recent kinetic isotope effect (KIE) studies have shown that many SNAr reactions are actually concerted. However, it remains unclear how variations in substrate structure affect whether a reaction is stepwise, concerted, or borderline. In this paper, we show that reactions between indole and moderately electron-deficient aryl fluorides proceed by a borderline mechanism and are subject to general base catalysis. These findings are consistent with density functional theory (DFT) calculations, which also predict that borderline mechanisms are operative for a broad range of industrially relevant SNAr reactions involving azole nucleophiles. The predicted transition structures vary smoothly independent of the mechanism, suggesting that these SNAr reactions exist on a mechanistic continuum. The findings of widespread general base catalysis and a mechanistic continuum will guide future efforts to devise general models of SNAr reactivity.

TS-tools: Rapid and automated localization of transition states based on a textual reaction SMILES input

Here, TS-tools is presented, a Python package facilitating the automated localization of transition states (TS) based on a textual reaction SMILES input. TS searches can either be performed at xTB or DFT level of theory, with the former yielding guesses at marginal computational cost, and the latter directly yielding accurate structures at greater expense. On a benchmarking dataset of mono- and bimolecular reactions, TS-tools reaches an excellent success rate of 95% already at xTB level of theory. For tri- and multimolecular reaction pathways - which are typically not benchmarked when developing new automated TS search approaches, yet are relevant for various types of reactivity, cf. solvent- and autocatalysis and enzymatic reactivity - TS-tools retains its ability to identify TS geometries, though a DFT treatment becomes essential in many cases. Throughout the presented applications, a particular emphasis is placed on solvation-induced mechanistic changes, another issue that received limited attention in the automated TS search literature so far.

Photochemical Degradation of the New Nicotine Pesticide Acetamiprid in Water

Acetamiprid is a novel nicotinic pesticide widely used in modern agriculture because of its low toxicity and specific biological target properties. The objective of this study was to understand the photolysis pattern of acetamiprid in the water column and elucidate its degradation products and mechanism. It was observed that acetamiprid exhibited different photolysis rates under different light source conditions in pure water, with ultraviolet > fluorescence > sunlight; furthermore, its photolysis half-life ranged from 17.3 to 28.6 h. In addition, alkaline conditions (pH 9.0) accelerated its photolysis rate, which increased with pH. Using gas chromatography-mass spectrometry, five direct photolysis products generated during the exposure of acetamiprid to pure water were successfully separated and identified. The molecular structure of acetamiprid was further analyzed using density functional theory, and the active photodegradation sites of acetamiprid were predicted. The mechanism of the photolytic transformation of acetamiprid in water was mainly related to hydroxyl substitution and oxidation. Based on these findings, a comprehensive transformation pathway for acetamiprid was proposed.

The electrophilic aromatic bromination of benzenes: mechanistic and regioselective insights from density functional theory

The HBr-assisted electrophilic aromatic bromination of benzene, anisole and nitrobenzene was investigated using static DFT calculations in gas phase and implicit apolar (CCl4) and polar (acetonitrile) solvent models at the ωB97X-D/cc-pVTZ level of theory. The reaction profiles corresponding to either a direct substitution reaction or an addition-elimination process were constructed and insight into the preferred regioselectivity was provided using a combination of conceptual DFT reactivity indices, aromaticity indices, Wiberg bond indices and the non-covalent interaction index. Our results show that under the considered reaction conditions the bromination reaction preferentially occurs through an addition-elimination mechanism and without formation of a stable charged Wheland intermediate. The ortho/para directing effect of the electron-donating methoxy-group in anisole was ascribed to a synergy between strong electron delocalisation and attractive interactions. In contrast, the preferred meta-addition on nitrobenzene could not be traced back to any of these effects, nor to the intrinsic reactivity property of the reactant. In this case, an electrostatic clash between the ipso-carbon of the ring and the nitrogen atom resulting from the later nature of the rate-determining step, with respect to anisole, appeared to play a crucial role.

Effect of Substituents on Molecular Reactivity during Lignin Oxidation by Chlorine Dioxide: A Density Functional Theory Study

Lignin is a polymer with a complex structure. It is widely present in lignocellulosic biomass, and it has a variety of functional group substituents and linkage forms. Especially during the oxidation reaction, the positioning effect of the different substituents of the benzene ring leads to differences in lignin reactivity. The position of the benzene ring branched chain with respect to methoxy is important. The study of the effect of benzene substituents on the oxidation reaction's activity is still an unfinished task. In this study, density functional theory (DFT) and the m062x/6-311+g (d) basis set were used. Differences in the processes of phenolic oxygen intermediates formed by phenolic lignin structures (with different substituents) with chlorine dioxide during the chlorine dioxide reaction were investigated. Six phenolic lignin model species with different structures were selected. Bond energies, electrostatic potentials, atomic charges, Fukui functions and double descriptors of lignin model substances and reaction energy barriers are compared. The effects of benzene ring branched chains and methoxy on the mechanism of chlorine dioxide oxidation of lignin were revealed systematically. The results showed that the substituents with shorter branched chains and strong electron-absorbing ability were more stable. Lignin is not easily susceptible to the effects of chlorine dioxide. The substituents with longer branched chains have a significant effect on the flow of electron clouds. The results demonstrate that chlorine dioxide can affect the electron arrangement around the molecule, which directly affects the electrophilic activity of the molecule. The electron-absorbing effect of methoxy leads to a low dissociation energy of the phenolic hydroxyl group. Electrophilic reagents are more likely to attack this reaction site. In addition, the stabilizing effect of methoxy on the molecular structure of lignin was also found.

A Lewis Acid Stabilized Ketenimine in an Unusual Variant of the Electrophilic Aromatic Substitution

Electrophilic aromatic substitution (EAS) can provide a straightforward approach to the efficient synthesis of functionalized complex aromatic molecules. In general, Lewis acids serve as a beneficial stimulus for the formation of a Wheland complex, the intermediate in the classical SE Ar mechanism of EAS, which is responsible for H/E (E=electrophile) substitution under formal H+ elimination. Herein, we report an unusual variant of EAS, in which a complex molecule such as the tricyanomethane, HC(CN)3 , is activated with a strong Lewis acid (B(C6 F5 )3 ) to the point where it can finally be used in an EAS. However, the Lewis acid here causes the isomerization of the tricyanomethane to the ketenimine, HN=C=C(CN)2 , which in turn directly attacks the aromatic species in the EAS, with simultaneous proton migration of the aromatic proton to the imino group, so that no elimination occurs that is otherwise observed in the SE Ar mechanism. By this method, it is possible to build up amino-malononitrile-substituted aromatic compounds in one step.

Cascade Nucleophilic Attack/Addition Cyclization Reactions to Synthesize Oxazolidin-2-imines via (Z)-2-Bromo-3-phenylprop-2-en-1-ols/3-phenylprop-2-yn-1-ols and Diphenyl Carbodiimides

Two concise strategies to synthesize oxazolidin-2-imines by cascade nucleophilic attack/addition cyclization reactions of (Z)-2-bromo-3-phenylprop-2-en-1-ols/3-phenylprop-2-yn-1-ols and diphenyl carbodiimides without a transition-metal catalyst have been developed. The reactions exhibited good substrate applicability tolerance, and a variety of substituted (Z)-4-((Z)-benzylidene)-N,3-diphenyloxazolidin-2-imines were synthesized in moderate to excellent yields with good stereoselectivity. The reports also provided a convenient strategy to synthesize 3-phenylprop-2-yn-1-ols by (Z)-2-bromo-3-phenylprop-2-en-1-ols. The economic and practical methods provide a great advantage for potential industrial synthesis of oxazolidin-2-imines.

Solvation in nitration of benzene and the valence electronic structure of the Wheland intermediate

Nitration of benzene is a representative aromatic substitution reaction related to the σ-complex (arenium ion or "Wheland" intermediate) concept. This reaction is typically carried out in a mixed acid solution to generate nitronium ions, and how solvent molecules play roles in the reaction has been of great interest. Here we will shed new light on the reaction, namely the electronic structure and the microscopic insights of the solvation, which have been rarely discussed so far. We studied this process using the reference interaction site model-self consistent field with constrained spatial electron density distribution (RISM-SCF-cSED) method, considering sulfuric acid or water molecules as a solvent. In this method, the electronic structure of the solute and the solvation structure are self-consistently determined based on quantum chemistry and statistical mechanics of molecular liquids. The solvation free energy surfaces in solution and solvation structures were verified. In the bond formation process of benzene and nitronium ions, the solvation structure by sulfuric acid molecules drastically changes and the solvation effect on the free energy is quite large. We revealed largely contributing resonance structures in the π-electron system of the σ-complex in gas and solution phases by analysing the valence electronic structures.