A DFT computational study of the molecular mechanism of [3 + 2] cycloaddition reactions between nitroethene and benzonitrile N-oxides

Energetic Aspects and Molecular Mechanism of 3-Nitro-substituted 2-Isoxazolines Formation via Nitrile N-Oxide [3+2] Cycloaddition: An MEDT Computational Study

Regioselectivity and the molecular mechanism of the [3+2] cycloaddition reaction between nitro-substituted formonitrile N-oxide 1 and electron-rich alkenes were explored on the basis of the wb97xd/6-311+G(d) (PCM) quantum chemical calculations. It was established that the thermodynamic factors allow for the formation of stable cycloadducts along all considered models. The analysis of the kinetic parameters of the main processes show that all [3+2] cycloadditions should be realized with full regioselectivity. In all cases, the formation of 5-substituted 3-nitro-2-isoxazolidines is clearly preferred. It is interesting that regiodirection is not determined by the local electrophile/nucleophile interactions but by steric effects. From a mechanistic point of view, all considered reactions should be treated as polar, one-step reactions. All attempts to locate the hypothetical zwitterionic intermediates along the cycloaddition paths were, however, not successful.

Discovery of 4-nitro-3-phenylisoxazole derivatives as potent antibacterial agents derived from the studies of [3 + 2] cycloaddition

Polysubstituted phenylisoxazoles were designed and synthesized to discover new antibacterial agents via [3 + 2] cycloaddition. Thirty-five compounds with a phenylisoxazole scaffold were characterized by NMR, HRMS, and X-ray techniques. After being evaluated against Xanthomonas oryzae (Xoo), Pseudomonas syringae (Psa), and Xanthomonas axonopodis (Xac), 4-nitro-3-phenylisoxazole derivatives were found to better antibacterial activities. Further studies have shown that the EC₅₀ values of these compounds were much better than that of the positive control, bismerthiazol.

Thirty-five compounds with phenylisoxazole scaffold were synthesized via [3+2] cycloaddition. After being evaluated against Xoo, Psa and Xac, 4-nitro-3-phenylisoxazole derivatives were found well antibacterial activities.

The Participation of 3,3,3-Trichloro-1-nitroprop-1-ene in the [3 + 2] Cycloaddition Reaction with Selected Nitrile N-Oxides in the Light of the Experimental and MEDT Quantum Chemical Study

The regioselective zw-type [3 + 2] cycloaddition (32CA) reactions of a series of aryl-substituted nitrile N-oxides (NOs) with trichloronitropropene (TNP) have been both experimentally and theoretically studied within the Molecular Electron Density Theory (MEDT). Zwitterionic NOs behave as moderate nucleophiles while TNP acts as a very strong electrophile in these polar 32CA reactions of forward electron density flux, which present moderate activation Gibbs free energies of 22.8-25.6 kcal·mol-1 and an exergonic character of 28.4 kcal·mol-1 that makes them irreversible and kinetically controlled. The most favorable reaction is that involving the most nucleophilic MeO-substituted NO. Despite Parr functions correctly predicting the experimental regioselectivity with the most favorable O-CCCl3 interaction, these reactions follow a two-stage one-step mechanism in which formation of the O-C(CCl3) bond takes place once the C-C(NO2) bond is already formed. The present MEDT concludes that the reactivity differences in the series of NOs come from their different nucleophilic activation and polar character of the reactions, rather than any mechanistic feature.

One-Pot and Two-Chamber Methodologies for Using Acetylene Surrogates in the Synthesis of Pyridazines and Their D-Labeled Derivatives

Acetylene surrogates are efficient tools in modern organic chemistry with largely unexplored potential in the construction of heterocyclic cores. Two novel synthetic paths to 3,6-disubstituted pyridazines were proposed using readily available acetylene surrogates through flexible C₂ unit installation procedures in a common reaction space mode (one-pot) and distributed reaction space mode (two-chamber): (1) an interaction of 1,2,4,5-tetrazine and its acceptor-functionalized derivatives with a CaC₂ -H₂ O mixture performed in a two-chamber reactor led to the corresponding pyridazines in quantitative yields; (2) [4+2] cycloaddition of 1,2,4,5-tetrazines to benzyl vinyl ether can be considered a universal synthetic path to a wide range of pyridazines. Replacing water with D₂ O and vinyl ether with its trideuterated analog in the developed procedures, a range of 4,5-dideuteropyridazines of 95-99% deuteration degree was synthesized for the first time. Quantum chemical modeling allowed to quantify the substituent effect in both synthetic pathways.

Initial Thermal Decomposition Mechanism of (NH2)2C=C(NO2)(ONO) Revealed by Double-Hybrid Density Functional Calculations

This work employs double-hybrid density functionals to re-examine the CO-NO bond dissociation mechanism of nitrite isomer of 1,1-diamino-2,2-dinitro-ethylene (DADNE) into (NH₂)₂C=C(NO₂)O and nitric monoxide (NO). The calculated results confirm that an activated barrier is present in the CO-NO bond dissociation process of (NH₂)₂C=C(NO₂)(ONO). Furthermore, it is proposed that a radical-radical adduct is involved in the exit dissociation path with subsequent dissociation to separate (NH₂)₂C=C(NO₂)O and NO radicals. The activation and reaction enthalpies at 298.15 K for the nitrite isomer dissociation are predicted to be 43.6 and 5.4 kJ mol^-1 at the B2PLYP/6-31G(d,p) level, respectively. Employing the B2PLYP/6-31G(d,p) reaction energetics, gradient, Hessian, and geometries, the kinetic model for the CO-NO bond dissociation of (NH₂)₂C=C(NO₂)(ONO) is obtained by a fitting to the modified Arrhenius form 1.05 × 10¹³(T/300)^0.39 exp[-27.80(T + 205.32)/R(T ² + 205.32²)] in units of per second over the temperature range 200-3000 K based on the canonical variational transition-state theory with multidimensional small-curvature tunneling.

Application of β-Phosphorylated Nitroethenes in [3+2] Cycloaddition Reactions Involving Benzonitrile N-Oxide in the Light of a DFT Computational Study

The regiochemistry of [3+2] cycloaddition (32CA) processes between benzonitrile N-oxide 1 and β-phosphorylated analogues of nitroethenes 2a–c has been studied using the Density Functional Theory (DFT) at the M062X/6-31+G(d) theory level. The obtained results of reactivity indices show that benzonitrile N-oxide 1 can be classified both as a moderate electrophile and moderate nucleophile, while β-phosphorylated analogues of nitroethenes 2a–c can be classified as strong electrophiles and marginal nucleophiles. Moreover, the analysis of CDFT shows that for [3+2] cycloadditions with the participation of β-phosphorylatednitroethene 2a and β-phosphorylated α-cyanonitroethene 2b, the more favored reaction path forms 4-nitro-substituted Δ2-isoxazolines 3a–b, while for a reaction with β-phosphorylated β-cyanonitroethene 2c, the more favored path forms 5-nitro-substituted Δ2-isoxazoline 4c. This is due to the presence of a cyano group in the alkene. The CDFT study correlates well with the analysis of the kinetic description of the considered reaction channels. Moreover, DFT calculations have proven the clearly polar nature of all analyzed [3+2] cycloaddition reactions according to the polar one-step mechanism.

Theoretical mechanistic study on the reaction of the methoxymethyl radical with nitrogen dioxide

Mechanism of the reaction of CH₃OCH₂ with NO₂ is explored theoretically at the M062X/MG3S and G4 levels. The calculated results indicate two stable association intermediates, CH₃OCH₂NO₂ (IM1) and CH₃OCH₂ONO (IM2), which can be produced by the attack of the nitrogen or oxygen atom of NO₂ to terminal carbon atom of CH₃OCH₂ without barrier involved. IM2 is found to take trans (IM2a)-cis (IM2b) conversion and isomerization to IM1, with the following stability order IM2a > IM2b > IM1. Starting from IM2a, the most feasible pathway is the direct O-NO bond cleavage leading to P1 (CH₃OCH₂O + NO) or the H-shift and O-NO bond rupture to produce P2 (CH₃OCHO + HNO), both of which have comparable contribution to the title reaction. There also involves an H-transfer from the methyl group of IM2a to the N atom with the simultaneous dissociations of the C-O and O-N bonds to produce P4 (2CH₂O + HNO). In addition, another dissociation pathway is open to IM2b which decompose to P5 (CH₂O + CH₃ONO) by the O-N and C-O bond scissions and the recombination of CH₃O and NO. Because all the intermediates and transition states involved in the above pathways lie below reactants, the CH₃OCH₂ + NO₂ reaction is expected to be rapid. Subsequent dissociation of IM1 and direct H-abstraction between CH₃OCH₂ and NO₂ are kinetically almost inhibited due to significantly high barriers. The present results can lead us to deeply understand the mechanism of the title reaction and may be helpful for understanding NO₂ combustion chemistry.

Understanding the molecular mechanism of the stereoselective conversion of N-trialkylsilyloxy nitronates into bicyclic isoxazoline derivatives

The conversion of N-trialkylsilyloxy nitronates into bicyclic isoxazoline derivatives has been explored using the density functional theory method within the context of molecular electron density theory at the ωB97XD(PCM)/6-311G(d,p) level.

Unprecedented Regio- and Stereoselective Synthesis of Pyrene-Grafted Dispiro[indoline-3,2'-pyrrolidine-3',3″-indolines]: Expedient Experimental and Theoretical Insights into Polar [3 + 2] Cycloaddition

A series of dispiro[indoline-3,2'-pyrrolidine-3',3″-indolines] was synthesized via a multicomponent polar [3 + 2] cycloaddition (32CA) reaction of isatin derivatives, sarcosine and (E)-3-(2-oxo-2-(pyren-1-yl)ethylidene)indolin-2-one derivatives. The regio- and stereochemistries of the cycloadducts were established on the basis of one-dimensional (1D) (1H-, 13C-, 13C-CRAPT NMR) and two-dimensional (2D) homonuclear and heteronuclear correlation NMR spectrometry experiments (1H-1H gDQFCOSY, 13C-1H-HSQCAD, 13C-1H-HMBCAD, 1H-1H-ROESYAD). The molecular mechanism and regio- and stereoselectivities of the cycloaddition (CA) reaction have been investigated utilizing a density functional theory (DFT) method and were thoroughly explained based on the transition-state stabilities and global/local electrophilicity/nucleophilicity reactivity indices of the reactants.

Molecular mechanism of Hetero Diels-Alder reactions between (E)-1,1,1-trifluoro-3-nitrobut-2-enes and enamine systems in the light of Molecular Electron Density Theory

The molecular mechanism of the reaction of (E)-1,1,1-trifluoro-3-nitrobut-2-ene 1 with 3,3-dimethyl-2-morpholinobutene 2 has been studied within the Molecular Electron Density Theory (MEDT). This theoretical study confirm the possibility of the formation of zwitterionic structures in the first reaction stage. Interestingly, that localized zwitterions are however not common intermediates for identified in the postreaction mixture products. The further Bonding Evolution Theory (BET) study show, that the key, HDA reaction takes place in one-step but in a non-concerted manner since three stages are clearly identified. First the C5-C6 double bond breaks, then the C1-C2 bond breaks, and in the last phase we observed the formation of the C1-C6 single bond and V(C2) and V' (C2) pseudoradical centers in Z1 molecule. In turn, the molecular mechanism of the conversion of zwitterion Z1 to product 3 can be divided also in three groups in which we observed the disappearance of the two pseudoradical centers and formation O4-C5 single and C3-N3 double bonds, respectively.

A DFT study on the molecular mechanism of the conjugated nitroalkenes polymerization process initiated by selected unsaturated nucleophiles

The participation of the nitroethene and its α-substituted analogs as model nitrofunctionalized monomers, and (Z)-C,N-diphenylnitrone and methyl vinyl ether as initiators in the polymerization reactions, has been analyzed in the framework of the density functional theory calculations at the M06-2X(PCM)/6-311 + G(d) level. Our computational study suggests the zwitterionic mechanism of the polymerization process. The exploration of the nature of critical structures shows that the first reaction stage exhibits evidently polar nature, whereas additions of further nitroalkene molecules to the polynitroalkyl molecular system formed should be considered as moderate polar processes. The more detailed view on the molecular transformations gives analysis based on the bonding evolution theory. This study shows that the case of polymerization reaction between nitroethene and (Z)-C,N-diphenylnitrone allows for distinguishing eleven topologically different phases, while, in the case of polymerization reaction nitroethene and methyl vinyl ether, we can distinguish nine different phases.

Theoretical analysis of the regio- and stereoselective synthesis of spiroisoxazolines

The [3+2] cycloaddition (32CA) reaction of benzonitrile oxide to α-methylene cyclopentanone and propionitrile oxide to γ-methyl-α-methylene-γ-butyrolactone, yielding regio- and stereochemically defined spiroisoxazolines, has been studied at the MPWB1K/6-311G(d,p) computational level. These processes proceed by a one-step mechanism through asynchronous transition states. Ortho regioselectivity and anti diastereofacial selectivity are predicted in complete agreement with the experimental outcomes.

Push-pull nitronates in the [3+2] cycloaddition with nitroethylene: Molecular Electron Density Theory study

The structure and the participation of the N-methoxy-N-[bis(methoxycarbonyl)methylene]amine N-oxide as model push-pull nitronate 1 with nitroethylene 2 in [3 + 2] cycloaddition (32CA) reaction have been analyzed within the Molecular Electron Density Theory (MEDT) using Density Functional Theory (DFT) calculations at the B3LYP(PCM)/6-31G(d) level. Topological analysis of the Electron Localization Function (ELF) of nitronate 1 reveals that this compound has pseudoradical center, while the conceptual DFT reactivity indices characterizes this three-atom-component (TAC) as a strong electrophile. The analyzed 32CA reaction takes place through a one-step mechanism. A Bonding Evolution Theory (BET) study of the more favorable reaction path associated with the 32CA reaction of nitronate 1 with nitroethylene 2 indicates that it is associated with a non-concerted two-stage one-step mechanism, in which the activation energy is mainly related with to the initial formation of the O3-C4 single bond. In the case of this reaction, an additional mechanism with formation of intermediate 7 is also found.

Regiospecific formation of the nitromethyl-substituted 3-phenyl-4,5-dihydroisoxazole via [3 + 2] cycloaddition

ABSTRACT

5-(Nitromethyl)-3-phenyl-4,5-dihydroisoxazole was obtained as a product of a high-yielding [3 + 2] cycloaddition reaction of in situ-generated benzonitrile N-oxide and 3-nitroprop-1-ene. For the first time, the regiochemistry of this reaction was unambiguously proven by X-ray structural analysis. The quantum-chemical calculation performed at the M06-2X/6-31G(d) (PCM) theoretical level affords a basis for explaining the course of reaction as well as the nature of transition states. Next, further DFT calculations together with spectral data shed light on structural aspects of the product.

GRAPHICAL ABSTRACT

Molecular Reactivity and Absorption Properties of Melanoidin Blue-G1 through Conceptual DFT

This computational study presents the assessment of eleven density functionals that include CAM-B3LYP, LC-wPBE, M11, M11L, MN12L, MN12SX, N12, N12SX, wB97, wB97X and wB97XD related to the Def2TZVP basis sets together with the Solvation Model Density (SMD) solvation model in calculating the molecular properties and structure of the Blue-G1 intermediate melanoidin pigment. The chemical reactivity descriptors for the system are calculated via the conceptual Density Functional Theory (DFT). The choice of the active sites related to the nucleophilic, electrophilic, as well as radical attacks is made by linking them with the Fukui function indices, the electrophilic Parr functions and the condensed dual descriptor Δ f ( r ) . The prediction of the maximum absorption wavelength tends to be considerably accurate relative to its experimental value. The study found the MN12SX and N12SX density functionals to be the most appropriate density functionals in predicting the chemical reactivity of the studied molecule.

Computational Prediction of the Protonation Sites of Ac-Lys-(Ala)n-Lys-NH2 Peptides through Conceptual DFT Descriptors

Six density functionals (M11, M11L, MN12L, MN12SX, N12, and N12SX) in connection with the Def2TZVP basis set and the SMD solvation model (water as a solvent) have been assessed for the calculation of the molecular structure and properties of several peptides with the general formula Ac-Lys-(Ala)n-Lys-NH2, with n = 0 to 5. The chemical reactivity descriptors for these systems have been calculated through Conceptual density functional theory (DFT). The active sites for nucleophilic and electrophilic attacks have been chosen by relating them to the Fukui function indices, the condensed dual descriptor Δf(r), and the electrophilic Parr functions. The results allowed the prediction of the protonation sites of the peptides and rendered a qualitative explanation of the difference in pKa of the two Lys groups.