SN2 Mechanism Research Articles

Palladium Single Atom-supported Covalent Organic Frameworks for Aqueous-phase Hydrogenative Hydrogenolysis of Aromatic Aldehydes via Hydrogen Heterolysis.

Developing a method for the tandem hydrogenative hydrogenolysis of bio-based furfuryl aldehydes to methylfurans is crucial for synthesizing sustainable biofuels and chemicals; however, it poses a challenge due to the easy hydrogenation of the C=C bond and difficult cleavage of the C-O bond. Herein, a palladium (Pd) single-atom-supported covalent organic framework was fabricated and showed a unique 2,5-dimethylfuran yield of up to 98.2% when reacted with 5-methyl furfuryl aldehyde in an unprecedented water solvent at 30°C. Furthermore, it exhibited excellent catalytic universality while converting various furfuryl-, benzyl-, and heterocyclic aldehydes at room temperature. The analysis of the catalytic mechanism confirmed that H2 was heterolytically activated on the Pd-N pair and triggered the keto-enol tautomerism of the covalent organic frameworks (COFs) host, resulting in H--Pd∙∙∙O-H+ sites. These sites served as novel asymmetric hydrogenation sites for the C=O group and hydrogenolysis sites for the C-OH group through a scarce SN2 mechanism. This study demonstrated remarkable bifunctional catalysis through the H2-induced keto-enol tautomerism of COF catalysts for the atypical preparation of methyl aromatics in a water solvent at room temperature.

Palladium Single Atom‐supported Covalent Organic Frameworks for Aqueous‐phase Hydrogenative Hydrogenolysis of Aromatic Aldehydes via Hydrogen Heterolysis

Developing a method for the tandem hydrogenative hydrogenolysis of bio‐based furfuryl aldehydes to methylfurans is crucial for synthesizing sustainable biofuels and chemicals; however, it poses a challenge due to the easy hydrogenation of the C=C bond and difficult cleavage of the C–O bond. Herein, a palladium (Pd) single‐atom‐supported covalent organic framework was fabricated and showed a unique 2,5‐dimethylfuran yield of up to 98.2% when reacted with 5‐methyl furfuryl aldehyde in an unprecedented water solvent at 30°C. Furthermore, it exhibited excellent catalytic universality while converting various furfuryl‐, benzyl‐, and heterocyclic aldehydes at room temperature. The analysis of the catalytic mechanism confirmed that H2 was heterolytically activated on the Pd–N pair and triggered the keto‐enol tautomerism of the covalent organic frameworks (COFs) host, resulting in H––Pd∙∙∙O–H+ sites. These sites served as novel asymmetric hydrogenation sites for the C=O group and hydrogenolysis sites for the C–OH group through a scarce SN2 mechanism. This study demonstrated remarkable bifunctional catalysis through the H2‐induced keto‐enol tautomerism of COF catalysts for the atypical preparation of methyl aromatics in a water solvent at room temperature.

Frustrated Lewis Pair-Promoted Organocatalytic Transformation of Hydrosilanes into Silanols with Water Oxidant.

Owing to their unique properties, the silanols have attracted intense attention but remain challenging to prepare from the organocatalytic oxidation of hydrosilanes using H2O as a green oxidant. Herein, we employ a frustrated Lewis pair (FLP) to successfully suppress the formation of undesired siloxanes and produce silanols in high to excellent yields in the presence of H2O. Mechanistic studies suggest that the reaction is initiated with the activation of FLP by H2O rather than by silanes and goes through a concerted SN2 mechanism. More importantly, the combination of the FLP-catalyzed oxidation of hydrosilanes with B(C6F5)3-catalyzed dehydrogenation enables us to realize the precise synthesis of sequence-controlled oligosiloxanes. This method exhibits a broad substrate scope and can be easily scaled up, thus exhibiting promising application potentials in the precision synthesis of silicon-containing polymer materials.

On the Origin of Enantioselectivity in Chiral Zeolite Asymmetric Catalyst GTM-3: Host-Guest Transfer of Chirality.

Knowledge of how extra-large-pore chiral zeolite asymmetric catalysts based on the -ITV framework imprint their chirality during a catalytic reaction is crucial in order to spread the scope for the catalytic enantioselective production of chiral compounds of interest. In this work, we have carried out a combined experimental and computational study on the catalytic activity of antipode GTM-3 catalysts during the ring-opening of trans-stilbene oxide with 1-butanol. Identification of the enantiomers of all the chiral species unraveled a surprising catalytic behavior: these chiral catalysts promote the transformation of one enantiomer of trans-stilbene oxide in the corresponding unlike product (with inversion of configuration of the attacked C) via an SN2 mechanism, and at the same time, the transformation of the other enantiomer of trans-stilbene oxide via an SN1-like mechanism into the like (with retention of configuration) and secondary products (diphenylacetaldehyde via Meinwald rearrangement and derived products). A computational study based on DFT + D methods suggested a potential explanation for this catalytic behavior, associated with a different orientation of trans-stilbene oxide enantiomers bound on the Ge(T7) positions in d4r units, which is stabilized by the development of intraframework H-bonds between the interrupted T7OH adjacent positions characteristic of this framework. Calculations suggest that each enantiomer of trans-stilbene oxide follows a different reaction pathway, one favoring the SN2 route by addition of butanol from the opposite side to form unlike-products, while the different orientation of the antipode enantiomer disfavors such SN2 route mainly by steric repulsions and at the same time favors the reaction toward the SN1 mechanism to give like- and secondary-products. Our study suggests that the strong enantioselectivity of GTM-3 catalysts for this reaction is associated with the particular orientation adopted by the chiral reactants within the chiral nanospace provided by the -ITV framework, similarly to what occurs with enzymes, and such preferential orientation is directly controlled by the asymmetric cavities where the reaction takes place, by the particular features of the Ge active sites in adjacent interrupted positions and by the presence of several framework OH groups in the nearby nanospace that interact with guest species. The experimental observations and the reaction mechanism proposed suggest that GTM-3 catalysts prepared from the (1S,2S) enantiomer of the N,N-ethyl-methyl-pseudoephedrinium organic agent should be enriched in the P4332 enantiomorphic space group of the -ITV framework and GTM-3 prepared from the (1R,2R) enantiomer in the antipode P4132. Interestingly, resolution of the absolute configuration of GTM-3 materials from 3D-electron diffraction data has been accomplished and confirms such an assignment, giving an average 82% enantio-enrichment in the corresponding chiral polymorph. Structure-solution of the location of the chiral structure-directing agents indicates that the transfer of chirality from the molecular component to the zeolite polymorph is governed by the development of strong H-bonds between the molecular hydroxyl group and the interrupted T(7)OH framework positions.

Facile preparation of fluorine-containing 2,3-epoxypropanoates and their epoxy ring-opening reactions with various nucleophiles.

We describe herein a facile method to access 2,3-epoxyesters with fluorine-containing substituents at their 3-position starting from the corresponding enoates by utilization of the low-costed and easy-to-handle reagent, NaOCl·5H2O. Because very little has been disclosed about the reactivity of such 2,3-epoxyesters, their epoxy ring opening by a variety of nucleophiles was carried out and we succeeded in clarifying these chemo- as well as regioselective processes proceeding via the SN2 mechanism to mainly afford 2-substituted 3-hydroxyesters usually in a highly anti selective manner.

In silico investigation on the separation of disulfide bonds by N-heterocyclic carbene.

Herein, the separation of a disulfide bond using different nucleophilic agents like tri-methyl phosphine (TMP), tris (2-carboxyethyl) phosphine (TCEP), and N-heterocyclic carbene (NHC) has been investigated. Both TMP and TCEP have demonstrated their ability to break disulfide bonds through the SN2 mechanism. However, it is worth noting that these reactions are endothermic. While searching for a suitable nucleophile, it was observed that the NHC-mediated reaction was exothermic. The natural bond orbital (NBO), principal interacting orbital (PIO) and extended transition state-natural orbitals for chemical valence (ETS-NOCV) studies help understand the electron transfer process between interacting orbitals during the chemical reactions.

Unveiling the Influence of Water Molecules for NF3 Removal by the Reaction of NF3 with OH: A DFT Study.

The removal of nitrogen trifluoride (NF3) is of significant importance in atmospheric chemistry, as NF3 is an important anthropogenic greenhouse gas. However, the radical species OH and O(1D) in atmospheric conditions are nonreactive towards NF3. It is necessary to explore possible ways to remove NF3 in atmosphere. Therefore, the participation of water molecules in the reaction of NF3 with OH was discussed, as water is abundant in the atmosphere and can form very stable complexes due to its ability to act as both a hydrogen bond donor and acceptor. Systemic DFT calculations carried out at the CBS-QB3 and ωB97XD/aug-cc-pVTZ level of theory suggest that water molecules could affect the NF3 + OH reaction as well. The energy barrier of the SN2 mechanism was decreased by 8.52 kcal/mol and 10.58 kcal/mol with the assistance of H2O and (H2O)2, respectively. Moreover, the presence of (H2O)2 not only reduced the energy barrier of the reaction, but also changed the product channels, i.e., formation of NF2O + (H2O)2-HF instead of NF2OH + (H2O)2-F. Therefore, the removal of NF3 by reaction with OH is possible in the presence of water molecules. The results presented in this study should provide useful information on the atmospheric chemistry of NF3.

Synthesis of novel chromeno-tethered imidazolone scaffold through one pot sequential multicomponent reaction mediated cyclization: A structural, computational and in silico investigation

A novel chromeno imidazole-based derivative was synthesized and characterized using single crystal X-ray diffraction technique. The MCR strategical methodology followed by the cyclization and the SN2 mechanism resulted in the formation of chromenoimidazolone molecular scaffold. The structural analysis revealed that the structure crystallizes in P1¯ space group and was stabilized by intra and intermolecular interactions. The dihedral angle of 82.85° indicated the non planarity of the molecule. The molecular interactions exhibited by the crystal structure were analysed by the Hirshfeld surface analysis and the H…H interactions was found to be major contributor to the overall interactions of the compound with the percentage contribution of 52.3%. The theoretical investigations were carried out using density functional theory calculations to predict various electronic properties of the compound. The HOMO-LUMO energy gap of the compound is found to be 1.4534 eV for alpha and 3.9367 eV for a beta spin. The MEP analysis revealed that the C = O exhibit the highest negative electrostatic potential with the value of -0.064 a.u. indicating its nucleophilic nature. Further, natural bond orbital analysis revealed that the LP(1)→π* interaction demonstrates the highest stabilization energy of 53.49 kcal/mol.The results of the molecular docking analysis of the compound against 6FS1 protein showed a docking score of -7.4 kcal/mol, indicating the potential of the compound to be a good anti-cancer agent. Further, the findings of the molecular docking were substantiated by the molecular dynamics simulation studies which showed very good stability of the protein-ligand complex.

Thermal instability of 1-butyl-3-methylimidazolium chloride ionic liquid

The evaporation and thermal decomposition (thermolysis) of 1-butyl-3-methylimidazolium chloride ionic liquid, [BuMIm][Cl](l), were studied in the temperature range of 373–463 K by thermogravimetry–mass spectrometry (TG–MS) and Knudsen cell mass spectrometry (KCMS) methods. The saturated vapor pressures and the enthalpy of vaporization of [BuMIm][Cl](l) were determined within 373–398 K, where the thermolysis of this ionic liquid occurs via the SN2 mechanism at a low rate. With increasing temperature, the thermolysis becomes more extensive, which is accompanied by the C2-methylation of [BuMIm][Cl](l). The resulting ion pairs [BuMMIm+][Cl-] are thermally unstable and decomposed. A decrease in the vapor pressure of the ion pairs [BuMIm+][Cl-] at a constant temperature takes place due to side reactions, resulting in the suppression of the evaporation. Complex ionic compounds were found in the thermolysis/evaporation residues using atmospheric pressure chemical ionization (APCI) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) methods. The priority and possible pathways of reactions involving ion pairs and the thermolysis products were established by quantum chemical calculations.

Mechanistic insight into benzylidene-directed glycosylation reactions using cryogenic infrared spectroscopy

The stereoselective formation of 1,2-cis glycosidic linkages is challenging. The currently most widely used strategy for their installation uses 4,6-O-benzylidene-protected building blocks. The stereoselectivity of this reaction is thought to be driven by a covalent intermediate, which reacts via an SN2 mechanism. However, the role of cationic SN1-type intermediates in this reaction is unclear. Here we elucidate the structure of glycosyl cations carrying 4,6-O-benzylidene groups using cryogenic infrared ion spectroscopy and computational methods. The data reveal that the intermediates form anhydro cations, which correlates well with the stereoselective outcome of SN1-type glycosylations. The study highlights how cryogenic infrared spectroscopy can elucidate the role of intermediates in sugar chemistry and how these structural data can be linked to reactions in solution.

Hypervalent Iodine-Catalyzed Fluorination of Diene-Containing Compounds: A Computational Study.

Studies have shown that the incorporation of fluorine into materials can improve their properties, but C-F bonds are not readily formed in nature. Although some researchers have studied the reaction of fluorinating alkenes catalyzed by hypervalent iodine, far too little attention has been paid to its reaction mechanism. This study aimed to explore the mechanism of the hypervalent iodine-catalyzed 1,4-difluorination of dienes. We found that the catalyst is favorable for the activation of C1=C2 double bonds through halogen bonds, and then two HFs interact with one F atom in the catalyst via hydrogen bonds, resulting in the cleavage of I-F bonds and the formation of [F-H∙∙∙F]-. Subsequently, the catalyst interacts with C1, and the roaming [F-H···F]- attacks C4 from the opposite side of the catalyst. After the fluorination step is completed, the nucleophile F- substitutes the catalyst via the SN2 mechanism. Our calculations demonstrated that the interaction between HF and F- is favorable for the stabilization of the transition state within the fluorination process for which the presence of two HFs in the reaction is the best. We also observed that [F-H∙∙∙F]- attacking C4 from the opposite side of the catalyst is more advantageous than attacking from the same side. This study therefore offers a novel perspective on the mechanism of the hypervalent iodine-catalyzed fluoridation of dienes.

Theoretical calculation study on the reaction mechanism of methanol/dimethyl ether carbonylation catalyzed by the B/Al/Ga-MOR zeolites

The reaction mechanism of methanol/dimethyl ether (DME) carbonylation catalyzed by isomorphously substituted B-, Al-, and Ga-MOR zeolites (B/Al/Ga-MOR) was comparatively investigated by the density functional theory (DFT) calculations. The commonalities and differences between methanol and dimethyl ether as the reactant as well as among various MOR zeolites in the catalytic reaction pathways were disclosed, where one Si atom was substituted by B, Al or Ga at the 8-ring side pockets T3 sites or the 12-ring channels T4 sites of MOR. The results indicate that the insertion of CO into methoxy group to form acetyl groups follows the SN2 mechanism and is the rate-determining step in the carbonylation reactions. Under 473 K, either methanol or dimethyl ether is used as feedstock, the formed acetyl group prefers to interact with CH3O in methanol to form methyl acetate. The T3 sites show better carbonylation selectivity, whereas T4 sites display better trimethoxonium ions selectivity which favors the generation of aromatics and leads to the catalyst deactivation. Comparing with Al-MOR, the introduction of Ga and B at the T3 sites increases the free energy barriers of carbonylation, whereas the introduction of Ga and B in particular at the T4 sites can substantially increase the energy barriers of generating trimethyloxonium ions, which can effectively suppress the side reaction and improve the catalyst stability. This work contributes to the understanding of the catalytic roles of various acidic sites in different channels of the MOR zeolites and provides certain theoretical support for tailoring and designing efficient MOR zeolite catalysts for methanol/dimethyl ether carbonylation.

Exploring borderline SN1-SN2 mechanisms: the role of explicit solvation protocols in the DFT investigation of isopropyl chloride.

Nucleophilic substitution at saturated carbon is a crucial class of organic reactions, playing a pivotal role in various chemical transformations that yield valuable compounds for society. Despite the well-established SN1 and SN2 mechanisms, secondary substrates, particularly in solvolysis reactions, often exhibit a borderline pathway. A molecular-level understanding of these processes is fundamental for developing more efficient chemical transformations. Typically, quantum-chemical simulations of the solvent medium combine explicit and implicit solvation methods. The configuration of explicit molecules can be defined through top-down approaches, such as Monte Carlo (MC) calculations for generating initial configurations, and bottom-up methods that involve user-dependent protocols to add solvent molecules around the substrate. Herein, we investigated the borderline mechanism of the hydrolysis of a secondary substrate, isopropyl chloride (iPrCl), at DFT-M06-2X/aug-cc-pVDZ level, employing explicit and explicit + implicit protocols. Top-down and bottom-up approaches were employed to generate substrate-solvent complexes of varying number (n = 1, 3, 5, 7, 9, and 12) and configurations of H2O molecules. Our findings consistently reveal that regardless of the solvation approach, the hydrolysis of iPrCl follows a loose-SN2-like mechanism with nucleophilic solvent assistance. Increasing the water cluster around the substrate in most cases led to reaction barriers of ΔH‡ ≈ 21 kcal mol-1, with nine water molecules from MC configurations sufficient to describe the reaction. The More O'Ferrall-Jencks plot demonstrates an SN1-like character for all transition state structures, showing a clear merged profile. The fragmentation activation strain analyses indicate that energy barriers are predominantly controlled by solvent-substrate interactions, supported by the leaving group stabilization assessed through CHELPG atomic charges.

Insights into the Zintl Cluster Mediated Disulfide Bond Separation: A DFT Study

AbstractDisulfide bond cleavage plays a crucial role in various chemical and biological processes. In recent years, developing novel and efficient catalysts for disulfide bond cleavage has garnered significant attention. This manuscript presents a comprehensive density functional theory (DFT) study on the separation of a disulfide bond by a well‐known Nona‐silicide Zintl cluster, Si94−. It is a single‐step exothermic reaction process that proceeds via the SN2 mechanism. This study also investigates the electronic activity, electron transfer process, and other electronic properties associated with the disulfide bond dissociation by the Si9‐Zintl cluster using the M06‐2X computational method.

Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom.

DNA synthesis catalyzed by DNA polymerase is essential for all life forms, and phosphodiester bond formation with phosphorus center inversion is a key step in this process. Herein, by using a single-selenium-atom-modified dNTP probe, we report a novel strategy to visualize the reaction stereochemistry and catalysis. We capture the before- and after-reaction states and provide explicit evidence of the center inversion and in-line attacking SN2 mechanism of DNA polymerization, while solving the diastereomer absolute configurations. Further, our kinetic and thermodynamic studies demonstrate that in the presence of Mg2+ ions (or Mn2+), the binding affinity (Km) and reaction selectivity (kcat/Km) of dGTPαSe-Rp were 51.1-fold (or 19.5-fold) stronger and 21.8-fold (or 11.3-fold) higher than those of dGTPαSe-Sp, respectively, indicating that the diastereomeric Se-Sp atom was quite disruptive of the binding and catalysis. Our findings reveal that the third metal ion is much more critical than the other two metal ions in both substrate recognition and bond formation, providing insights into how to better design the polymerase inhibitors and discover the therapeutics.

Insights into the Friedel-Crafts Benzoylation of N-Methylpyrrole inside the Confined Space of the Self-Assembled Resorcinarene Capsule.

Friedel-Crafts benzoylation of N-methylpyrrole 2 can run inside the confined space of the hexameric resorcinarene capsule C. The bridged water molecules at the corner of C act as H-bonding donor groups to polarize the C-Cl bond of benzoyl chlorides 3a-f. Confinement effects on the regiochemistry of the FC benzoylation of N-methylpyrrole are observed. The nature of the para-substituents of 3a-f and their ability to establish H-bonds with the water molecules of C work synergistically with the steric constrictions imposed by the capsule to drive the regiochemistry of products 4a-f. QM investigations indicate that inside the cavity of C, the FC benzoylation of 2 has a bimolecular concerted SN2 mechanism, appropriately, above-plane nucleophilic vinylic substitution (SNVπ)─supported by H-bonding interactions between water molecules and both the leaving Cl atom and the carbonyl group.

2,2'-Dithiobispyrazine: about the disulfide bond.

X-ray diffraction studies reveal that pyrazine-2-thiol undergoes condensation to 2,2'-dithiobispyrazine [systematic name: 2-(pyrazin-2-yldisulfanyl)pyrazine], C8H6N4S2 (I), under aerial conditions. In the molecule of I, the pyrazine rings are arranged in an almost perpendicular manner, with an absolute value of the C-S-S-C torsion angle of -91.45 (6)°. A search in the Cambridge Structural Database confirmed that such a conformation is typical for disulfide compounds. Three different rotamers of disulfide I were studied using quantum theoretical studies. The rotamer of lowest energy was observed in the crystalline state in the structure stabilized by hydrogen-bond, chalcogen-bond and stacking interactions. Further quantum chemical computations confirm that 2,2'-dithiobispyrazine can react according to the SN2 mechanism.

A mechanistic insight for the biosynthesis of N,N-dimethyltryptamine: An ONIOM theoretical approach

Psychoactive natural products are potent serotonergic agonists capable of modulating brain functions such as memory and cognition. These substances have shown therapeutic potential for treating various mental disorders. The fact that N,N-dimethyltryptamine (DMT) is produced endogenously in several plants and animals, including humans, makes it particularly attractive. As an amino acid-derived alkaloid, the DMT biosynthetic pathway is part of the L-tryptophan biochemical cascade and can be divided into the decarboxylation by an aromatic L-amino acid decarboxylase (AADC) for tryptamine formation and the subsequent double-methylation by the indolethylamine-N-methyltransferase (INMT) through the cofactor S-adenosyl-L-methionine (SAM), a methyl donor. Unlike the decarboxylation mechanism of L-tryptophan, the molecular details of the double methylation of tryptamine have not been elucidated. Therefore, we propose an in silico model using molecular dynamics (MD), non-covalent interaction index (NCI) and density functional theory (DFT) calculations with the ONIOM QM:MM B3LYP/6-31+G(d,p):MM/UFF level of theory. Based on the obtained energetic data, the potential energy surface (PES) indicates an SN2 mechanism profile, with the second methylation energy barrier being the rate-limiting step with δG‡=60kJ∙mol−1 larger than the previous methylation, following the NCI analysis showing more repulsive interactions for the second transition state. In addition, the hybridization information of each reaction step provides geometric details about the double-methylation.

Using Stop Motion Animations to Activate and Analyze High School Students’ Intuitive Resources about Reaction Mechanisms

Mechanisms are part of the high school curriculum in many countries. Although research shows that university students struggle with mechanistic reasoning, very little is known about learning mechanisms in high school. Understanding the cognitive resources that high school students intuitively activate is critical to fostering meaningful learning. A readily available tool for modeling dynamic processes are stop-motion animations (SMAs). In this study, 55 high school students were asked to create SMAs of their intuitive ideas of nucleophilic substitution reactions. In a second step, the students evaluated two pre-made SMAs modeling the textbook-based stepwise (SN1) and concerted (SN2) mechanisms. Within the student-generated SMAs, SN1- and SN2-like mechanisms were equally distributed; after viewing the textbook-style animations, most students rated an SN2 mechanism as more likely. However, no group modeled both types of mechanisms or reasoned that both mechanisms were possible. Students used diverse chemical concepts as well as plausibility in their reasoning. However, simultaneous movement of atoms, conformational changes, and the idea of competing and boundary mechanisms do not seem intuitive. In conclusion, SMAs were found to be an appropriate tool for activating, analyzing, and discussing students’ resources “on the fly”, and these ideas can serve as a starting point for promoting productive mechanistic reasoning.

A New Approach to the Ring-Opening of Epoxides under Mild and Green Conditions

In this research work, we have designed and introduced [Zr-UiO-66-CO2H]Br as a versatile heterogeneous acid catalyst for the ring-opening of epoxides through SN1 and/or SN2 type mechanisms. In addition, the appropriate method for designing an active and efficient Bronsted acid site in metal-organic frameworks is discussed. [Zr-UiO-66-CO2H]Br was applied for the preparation of α-aryloxy alcohols by the condensation reaction of various epoxides with phenol or thiophenols under mild and green conditions.