Mechanism Of Nucleophilic Substitution Research Articles

Nucleophilic Displacement Reactions of Silver-Based Metal-Organic Chalcogenolates.

We report nucleophilic displacement reactions that can increase the dimensionality or coordination number of silver-based metal-organic chalcogenolates (MOChas). MOChas are crystalline ensembles containing one-dimensional (1D) or two-dimensional (2D) inorganic topologies with structures and properties defined by the choice of metal, chalcogen, and ligand. MOChas can be readily prepared from a variety of small-molecule ligands and metals or metal ions. Although MOChas offer ligand diversity, most reported examples use relatively small ligands, typically involving short alkyl chains, aryl rings, or molecular cages. This is because larger, more complex molecules often yield poor product morphologies with indeterminate structures. In this study, we overcame this limitation by employing a ligand exchange strategy whereby a 1D MOCha, silver(I) methyl 2-mercaptobenzoate (2MMB), is used as a silver source for preparing 2D examples. The reaction proceeds generally toward products composed of the stronger nucleophile. We show that the reaction prefers displacing 1D topologies to yield 2D ones and replacing thiolates with selenolates. We performed a study to characterize the mechanism by which organic chalcogenols and dichalcogenides exchange with MOChas. The collected data and product analysis support a proposed mechanism of nucleophilic substitution, explaining how both organic chalcogenols and dichalcogenides can displace ligands in MOChas. This work provides a new synthetic route that will enable the preparation of more elaborate MOChas and heterostructures thereof. This approach enabled the preparation of previously inaccessible oligophenyl MOChas, which were successfully solved via small-molecule serial femtosecond crystallography (smSFX) at the SPring-8 Ångström Compact Free Electron LAser (SACLA) facility.

Catalysis of an SN2 pathway by geometric preorganization.

Bimolecular nucleophilic substitution (SN2) mechanisms occupy a central place in the historical development and teaching of the field of organic chemistry1. Despite the importance of SN2 pathways in synthesis, catalytic control of ionic SN2 pathways is rare and notably uncommon even in biocatalysis2,3, reflecting the fact that any electrostatic interaction between a catalyst and the reacting ion pair necessarily stabilizes its charge and, by extension, reduces polar reactivity. Nucleophilic halogenase enzymes navigate this tradeoff by desolvating and positioning the halide nucleophile precisely on the SN2 trajectory, using geometric preorganization to compensate for the attenuation of nucleophilicity4. Here we show that a small-molecule (646 Da) hydrogen-bond-donor catalyst accelerates the SN2 step of an enantioselective Michaelis-Arbuzov reaction by recapitulating the geometric preorganization principle used by enzymes. Mechanistic and computational investigations show that the hydrogen-bond donor diminishes the reactivity of the chloride nucleophile yet accelerates the rate-determining dealkylation step by reorganizing both the phosphonium cation and the chloride anion into a geometry that is primed to enter the SN2 transition state. This new enantioselective Arbuzov reaction affords highly enantioselective access to an array of H-phosphinates, which are in turn versatile P-stereogenic building blocks amenable to myriad derivatizations. This work constitutes, to our knowledge, the first demonstration of catalytic enantiocontrol of the phosphonium dealkylation step, establishing a new platform for the synthesis of P-stereogenic compounds.

Acetal‐thiol Click‐like Reaction: Facile and Efficient Synthesis of Dynamic Dithioacetals and Recyclable Polydithioacetals

AbstractDithioacetals are heavily used in organic, material and medical chemistries, and exhibit huge potential to synthesize degradable or recyclable polymers. However, the current synthetic approaches of dithioacetals and polydithioacetals are overwhelmingly dependent on external catalysts and organic solvents. Herein, we disclose a catalyst‐ and solvent‐free acetal‐thiol click‐like reaction for synthesizing dithioacetals and polydithioacetals. High conversion, higher than acid catalytic acetal‐thiol reaction, can be achieved. High universality was confirmed by monitoring the reactions of linear and cyclic acetals (including renewable bio‐sourced furan‐acetal) with aliphatic and aromatic thiols, and the reaction mechanism of monomolecular nucleophilic substitution (SN1) and auto‐protonation (activation) by thiol was clarified by combining experiments and density functional theory computation. Subsequently, we utilize this reaction to synthesize readily recyclable polydithioacetals. By simple heating and stirring, linear polydithioacetals with w of ~110 kDa were synthesized from acetal and dithiol, and depolymerization into macrocyclic dithioacetal and repolymerization into polydithioacetal can be achieved; through reactive extrusion, a semi‐interpenetrating polymer dynamic network with excellent mechanical properties and continuous reprocessability was prepared from poly(vinyl butyral) and pentaerythritol tetrakis(3‐mercaptopropionate). This green and high‐efficient synthesis method for dithioacetals and polydithioacetals is beneficial to the sustainable development of chemistry.

Acetal-thiol Click-like Reaction: Facile and Efficient Synthesis of Dynamic Dithioacetals and Recyclable Polydithioacetals.

Dithioacetals are heavily used in organic, material and medical chemistries, and exhibit huge potential to synthesize degradable or recyclable polymers. However, the current synthetic approaches of dithioacetals and polydithioacetals are overwhelmingly dependent on external catalysts and organic solvents. Herein, we disclose a catalyst- and solvent-free acetal-thiol click-like reaction for synthesizing dithioacetals and polydithioacetals. High conversion, higher than acid catalytic acetal-thiol reaction, can be achieved. High universality was confirmed by monitoring the reactions of linear and cyclic acetals (including renewable bio-sourced furan-acetal) with aliphatic and aromatic thiols, and the reaction mechanism of monomolecular nucleophilic substitution (SN1) and auto-protonation (activation) by thiol was clarified by combining experiments and density functional theory computation. Subsequently, we utilize this reaction to synthesize readily recyclable polydithioacetals. By simple heating and stirring, linear polydithioacetals with w of ~110 kDa were synthesized from acetal and dithiol, and depolymerization into macrocyclic dithioacetal and repolymerization into polydithioacetal can be achieved; through reactive extrusion, a semi-interpenetrating polymer dynamic network with excellent mechanical properties and continuous reprocessability was prepared from poly(vinyl butyral) and pentaerythritol tetrakis(3-mercaptopropionate). This green and high-efficient synthesis method for dithioacetals and polydithioacetals is beneficial to the sustainable development of chemistry.

Discovery of a Tunable Heterocyclic Electrophile 4-Chloro-pyrazolopyridine That Defines a Unique Subset of Ligandable Cysteines.

Electrophilic small molecules with novel reactivity are powerful tools that enable activity-based protein profiling and covalent inhibitor discovery. Here, we report a reactive heterocyclic scaffold, 4-chloro-pyrazolopyridine (CPzP) for selective modification of proteins via a nucleophilic aromatic substitution (SNAr) mechanism. Chemoproteomic profiling reveals that CPzPs engage cysteines within functionally diverse protein sites including ribosomal protein S5 (RPS5), inosine monophosphate dehydrogenase 2 (IMPDH2), and heat shock protein 60 (HSP60). Through the optimization of appended recognition elements, we demonstrate the utility of CPzP for covalent inhibition of prolyl endopeptidase (PREP) by targeting a noncatalytic active-site cysteine. This study suggests that the proteome reactivity of CPzPs can be modulated by both electronic and steric features of the ring system, providing a new tunable electrophile for applications in chemoproteomics and covalent inhibitor design.

Regioselective amination of 4-methylene-5,7-dinitroquinazoline: a mechanistic consideration on non-conventional N-H—π interactions between amine and ethylene moiety

ABSTRACT Pi (π) interactions originating from the N-H bond of amine and ethylene moiety have been explored on the mechanism of aromatic nucleophilic substitution (ArSN) of the nitro group of 4-methylene-5,7-dinitroquinazoline with methylamine in the gas phase and solvent media within DFT framework. The free energy profiles confirmed that the amination should take place at peri-position and calculations support the one-step mechanism through a transition state with no intermediate in the reaction route. Stabilisation of peri-transition state by intramolecular weak interaction akin to hydrogen bonding N-H—CH2 = C leads to the regioselective amination at peri-position of 4-methylene-5,7-dinitroquinazoline. The intramolecular hydrogen bond interactions at N-H—CH2 = C in the peri-transition state are strongly supported by a red shift in N-H stretching vibrations in simulated IR spectra and are confirmed by studying energetics of amination of structural/electronic analogues of 4-methylene-5,7-dinitroquinazoline. The present study established that ethylene plays an important role as an efficient H-bond acceptor in fixing the regioselectivity at peri-position in the amination of 4-methylene-5,7-dinitroquinazoline. This is the first-ever report for the exploration of the role of ethylene moiety as a hydrogen bond acceptor in mediating the regioselectivity of organic reactions.

Intermolecular interaction of azide, cyano and alkyne-N-phenethylacetamide dimers: Experimental and quantum chemical approach

In this study, we present the synthesis and structure characterization by single-crystal X-ray Diffraction (SC-XRD), Ultraviolet Spectroscopy (UV), Fourier Transform Infrared Spectroscopy (FTIR), Nuclear Magnetic Resonance (NMR) and High-resolution Mass Spectrometry (HRMS) of 2-azido-N-phenethylacetamide (4) and 2-cyano-N-phenethylacetamide (6). Further, Density Functional Theory (DFT) was employed to get a better insight regarding the properties exhibited by the compounds. The computational chemistry has been used to explain and investigate the bimolecular nucleophilic substitution (SN2) and concerted acyl substitution mechanisms for the synthesis of compounds 4 and 6, respectively. Additionally, intrinsic reaction coordinate (IRC) calculations confirm the transition state for these reactions. The X-ray diffraction analysis showed that the compounds 4 and 6 crystallized as monoclinic systems, in space group P21/c and P21/n, respectively. The Hirshfeld Surface Analysis revealed that the main contributions in the crystal packing have H···H, H···N/N···H, H···C/C···H and H···O/O···H interactions. The frontier molecular orbital energies were calculated and the HOMO-LUMO energy gap of 4 and 6 were 10.011 and 10.278 eV, respectively. Theoretical values of electronic transitions, vibrational frequencies and NMR chemical shifts were calculated and compared with experimental results, they all showed good results.

Studying the Structure and Properties of Epoxy Composites Modified by Original and Functionalized with Hexamethylenediamine by Electrochemically Synthesized Graphene Oxide.

In this study, we used multilayer graphene oxide (GO) obtained by anodic oxidation of graphite powder in 83% sulfuric acid. The modification of GO was carried out by its interaction with hexamethylenediamine (HMDA) according to the mechanism of nucleophilic substitution between the amino group of HMDA (HMDA) and the epoxy groups of GO, accompanied by partial reduction of multilayer GO and an increase in the deformation of the carbon layers. The structure and properties of modified HMDA-GO were characterized using research methods such as scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction spectroscopy and Raman spectroscopy. The conducted studies show the effectiveness of using HMDA-OG for modifying epoxy composites. Functionalizing treatment of GO particles helps reduce the free surface energy at the polymer-nanofiller interface and increase adhesion, which leads to the improvement in physical and mechanical characteristics of the composite material. The results demonstrate an increase in the strength and elastic modulus in bending by 48% and 102%, respectively, an increase in the impact strength by 122%, and an increase in the strength and elastic modulus in tension by 82% and 47%, respectively, as compared to the pristine epoxy composite which did not contain GO-HMDA. It has been found that the addition of GO-HMDA into the epoxy composition initiates the polymerization process due to the participation of reactive amino groups in the polymerization reaction, and also provides an increase in the thermal stability of epoxy nanocomposites.

Bay-Substitution of Perylene Bisimides with Bidentate Nucleophiles: The Case of Aryloxide Anions.

In this study, we delve into the regioselectivity of nucleophilic reactions involving brominated perylene bisimides (PBIs) and various bidentate aryloxide anions, previously associated with an SRN1 mechanism. We present herein a new perspective, suggesting that a single-electron-transfer aromatic nucleophilic substitution (SeT-SNAr) mechanism is a more plausible scenario. Our study reveals the favorable impact of photostimulation on reaction yields, making our method a convenient approach for accessing O-arylated PBIs.

Fluorinated Benzimidazole-Linked Highly Conjugated Polymer Enabling Covalent Polysulfide Anchoring for Stable Sulfur Batteries.

Sulfur is one of the most abundant and economical elements in the p-block family and highly redox active, potentially utilizable as a charge-storing electrode with high theoretical capacities. However, its inherent good solubility in many electrolytes inhibits its accessibility as an electrode material in typical metal-sulfur batteries. In this work, the synthetically designed fluorinated porous polymer, when treated with elemental sulfur through a well-known nucleophilic aromatic substitution mechanism (SN Ar), allows for the covalent integration of polysulfides into a highly conjugated benzimidazole polymer by replacing the fluorine atoms. Chemically robust benzimidazole linkages allow such harsh post-synthetic treatment and facilitate the electronic activation of the anchored polysulfides for redox reactions under applied potential. The electrode amalgamated with sulfurized polymer mitigates the so-called polysulfide shuttle effect in the lithium-sulfur (Li-S) battery and also enables a reversible, more environmentally friendly, and more economical aluminum-sulfur (Al-S) battery that is configured with mostly p-block elements as cathode, anode, and electrolytes. The improved cycling stabilities and reduction of the overpotential in both cases pave the way for future sustainable energy storage solutions.

Iodometric determination of quinine sulfate in tablets using N-oxidation with diperoxysebacic acid

Using diperoxysebacic acid as an example, it was shown the interaction of diperoxycarboxylic acids with quinine alkaloid in an aqueous medium by kinetics method. The reaction proceeds quantitatively by the mechanism of nucleophilic substitution of β-peroxide oxygen atom in diperoxycarboxylic acid with the formation of the corresponding N-oxide, and the kinetics of the process is a subject to general rules of specific acid-base catalysis. New iodometric methods were developed, and the possibility of quinine sulfate quantification in pure form ‘Quinine sulfate’, as well as in the combined dosage form ‘Limpar® N 200 mg’ (Cassella Med GmbH, Germany) and in ‘Quinine sulfate 200 mg Tablets’ (Accord Healthcare Ltd, UK) by the reaction of oxidation with diperoxycarboxylic acid. They are characterized by high selectivity, and rate, simplicity of performing, and good accuracy. No toxic reagents or special conditions required. RSD ≤1.6% (δ =+0.40..+0.72%), LOQ=0.01 mg.

Multimeric structure of a subfamily III haloalkane dehalogenase-like enzyme solved by combination of cryo-EM and x-ray crystallography.

Haloalkane dehalogenase (HLD) enzymes employ an SN 2 nucleophilic substitution mechanism to erase halogen substituents in diverse organohalogen compounds. Subfamily I and II HLDs are well-characterized enzymes, but the mode and purpose of multimerization of subfamily III HLDs are unknown. Here we probe the structural organization of DhmeA, a subfamily III HLD-like enzyme from the archaeon Haloferax mediterranei, by combining cryo-electron microscopy (cryo-EM) and x-ray crystallography. We show that full-length wild-type DhmeA forms diverse quaternary structures, ranging from small oligomers to large supramolecular ring-like assemblies of various sizes and symmetries. We optimized sample preparation steps, enabling three-dimensional reconstructions of an oligomeric species by single-particle cryo-EM. Moreover, we engineered a crystallizable mutant (DhmeAΔGG ) that provided diffraction-quality crystals. The 3.3 Å crystal structure reveals that DhmeAΔGG forms a ring-like 20-mer structure with outer and inner diameter of ~200 and ~80 Å, respectively. An enzyme homodimer represents a basic repeating building unit of the crystallographic ring. Three assembly interfaces (dimerization, tetramerization, and multimerization) were identified to form the supramolecular ring that displays a negatively charged exterior, while its interior part harboring catalytic sites is positively charged. Localization and exposure of catalytic machineries suggest a possible processing of large negatively charged macromolecular substrates.

Novel cellulose derivative containing aminophenylacetic acid as sustainable adsorbent for removal of cationic and anionic dyes

The synthesis and characterization of a novel cellulose derivative as a potential sustainable adsorbent for cationic and anionic dyes are described through processing in ionic liquids. Cellulose was solubilized in ionic liquid with tosyl chloride to form tosyl cellulose which reacted with 4-aminophenylacetic acid through nucleophilic substitution mechanism. The new cellulose derivative was characterized and explored as an effective adsorbent for methylene blue (MB) and methyl orange (MO) removal, and the adsorption behaviors were investigated with various models. The adsorption behavior of the cellulose derivative followed Langmuir and pseudo-second-order models, and the maximum adsorption efficiency recorded 135 and 106 mg/g for MB and MO, respectively. There is possibility that the enhanced adsorption capacity of the cellulose derivative is due to the carboxylic and amino functional groups that provide sufficient active sites to enhance dye molecule affinity. The adsorption results demonstrate that the cellulose derivative containing aminophenylacetic acid was efficient adsorbent for removals of MB and MO.

Direct Acylation of Unactivated Alkyl Halides with Aldehydes through N‐Heterocyclic Carbene Organocatalysis

AbstractCatalytic acylation of organohalides with aldehydes is an ideal strategy for the direct synthesis of ketones. However, the utilization of unactivated alkyl halides in such a transformation remains a formidable challenge. In this study, we developed a cross‐coupling reaction of aldehydes with unactivated alkyl halides through N‐heterocyclic carbene catalysis. With this protocol, various ketones could be rapidly synthesized from readily available starting materials under mild conditions. This organocatalytic system was successfully applied in the late‐stage functionalization of pharmaceutical derivatives. Mechanistic investigations suggest a closed‐shell nucleophilic substitution mechanism for this reaction.

Direct Acylation of Unactivated Alkyl Halides with Aldehydes through N-Heterocyclic Carbene Organocatalysis.

Catalytic acylation of organohalides with aldehydes is an ideal strategy for the direct synthesis of ketones. However, the utilization of unactivated alkyl halides in such a transformation remains a formidable challenge. In this study, we developed a cross-coupling reaction of aldehydes with unactivated alkyl halides through N-heterocyclic carbene catalysis. With this protocol, various ketones could be rapidly synthesized from readily available starting materials under mild conditions. This organocatalytic system was successfully applied in the late-stage functionalization of pharmaceutical derivatives. Mechanistic investigations suggest a closed-shell nucleophilic substitution mechanism for this reaction.

Insight into etherification of 1,3-dimethylol-2-imidazolidinone with the primary alcohols and the hydroxyl groups of cellulose chain (n = 1–4) in acidic condition

Etherification of 1,3-dimethylol-2-imidazolidinone (DMEU) with the primary alcohols and the hydroxyl groups of cellulose chain (n = 1–4) in acidic condition were probed in both gas phase and water solvent by using the Onsager model and polarized continuum model (PCM). Geometry and energy of reactants, products, intermediate complexes, carbocation intermediate, and transition state (TS) structures were calculated by using the methods of MP2, B3LYP, PM3MM at the basis sets of 6-311+g (d), 6-311g (d,p). The computational results indicate that the etherification adheres to unimolecular nucleophilic substitution (SN1) mechanism; reactants and products can form the activated complexes with H+ ions in which H+ ions are occupied by the O-atom of CO group in the reactant complex and the product complex. Potential energy surface (PES) of the reaction has the triple-well shape. Effect of substituent R in primary alcohol R-CH2OH (R = H, CH3, CH2CH3, CH2OCH3, CH2F) on the reactivity is significant. The energy barrier of H+ ions releasing step is much higher than those of the activation steps. The calculational data is in the good agreement with the experimental data in the literature.

Theoretical Insight on the Formation Mechanism of a Trisubstituted Derivative of Closo-Decaborate Anion [B10H7O2CCH3(NCCH3)

A theoretical modelling of the interaction process between a protonated complex of carboxonium derivative [2,6-B10H8O2CCH3*Hfac]0 and acetonitrile molecule CH3CN was carried out. As a result of the process, a trisubstituted [B10H7O2CCH3(NCCH3)]0 derivative was formed. This reaction has an electrophile-induced nucleophilic substitution (EINS) mechanism. The main intermediates and transition states of the substitution process were established. As in the case of all previously investigated EINS processes, the key intermediate was an anion with a dihydrogen H2 fragment attached to one boron atom (B(H2) structure motif). The process of nucleophilic substitution can proceed on a different position of the cluster cage. The main potential pathways were assessed. It was established that substitution on the B4 position of the cluster cage was the most energetically favourable, and the [2,4,6-B10H7O2CCH3(NCCH3)]0 isomer was formed.

Radiation-Initiated Dehalogenation of Organofluorine Compounds in Aqueous Solutions

The γ-radiolysis of 2-fluoroethanol-1, 2,2,2-trifluoroethanol-1, 3-fluoropropanol-1, and 4,4,4- trif luorobutanol-1 in aqueous solutions in an inert atmosphere or in the presence of oxygen has been studied. It has been found that the dehalogenation of hydroxyl-containing organic compounds is induced by •ОН and Н• radicals rather than hydrated electrons. The carbon-centered α-hydroxy-β-fluoroethyl radicals FCH2–•CHOH are def luorinated much more efficiently than α-fluoroalkyl radicals, both vicinal (F–•CHCH2OH) and nonvicinal (F–•CHCH2CH2OH). In the absence of oxygen, α-fluoroalkyl radicalseliminate fluoride ions by the mechanism of nucleophilic substitution, and this process is enhanced in the presence of alkali. In an oxygenated medium, the dehalogenation of α-fluoroalkyl radicals occurs via the addition of oxygen molecules to them and the subsequent disproportionation of resulting peroxyl radicals. The dehalogenation of the α-hydroxy-β-fluoroethyl radicals FCH2–•CHOH is inhibited by oxygen through their oxidation.

A NIR fluorescent probe for imaging thiophenol in the living system and revealing thiophenol-induced oxidative stress

Thiophenol (PhSH) is an important raw material for organic synthesis, while its high toxicity to organisms makes it an environmental pollutant. Therefore, it is crucial to accurately detect PhSH and explore its metabolic process in the living system. Herein, a near-infrared (NIR) fluorescent probe TEM-FB was developed for sensing PhSH with a turn-on fluorescent signal at 719 nm and a large Stokes shift (198 nm) based on generating the intramolecular charge transfer (ICT) process. TEM-FB shows high specificity and significant sensitivity towards PhSH (detection limit: 10 nmol/L) via the aromatic nucleophilic substitution mechanism. Furthermore, it was successfully applied to image PhSH in multiple cell lines and in zebrafish. Notably, we revealed the oxidative stress process caused by PhSH and demonstrated that the hydrogen peroxide (H2O2) in cells would alleviate the poisonousness from exogenous PhSH for the first time. This work provides a promising bioimaging tool for monitoring PhSH in living systems and visualizing the process of oxidative stress induced by PhSH.

Synthesis of Disubstituted Carboxonium Derivatives of Closo-Decaborate Anion [2,6-B10H8O2CC6H5]-: Theoretical and Experimental Study.

A comprehensive study focused on the preparation of disubstituted carboxonium derivatives of closo-decaborate anion [2,6-B10H8O2CC6H5]- was carried out. The proposed synthesis of the target product was based on the interaction between the anion [B10H11]- and benzoic acid C6H5COOH. It was shown that the formation of this product proceeds stepwise through the formation of a mono-substituted product [B10H9OC(OH)C6H5]-. In addition, an alternative one-step approach for obtaining the target derivative is postulated. The structure of tetrabutylammonium salts of carboxonium derivative ((C4H9)4N)[2,6-B10H8O2CC6H5] was established with the help of X-ray structure analysis. The reaction pathway for the formation of [2,6-B10H8O2CC6H5]- was investigated with the help of density functional theory (DFT) calculations. This process has an electrophile induced nucleophilic substitution (EINS) mechanism, and intermediate anionic species play a key role. Such intermediates have a structure in which one boron atom coordinates two hydrogen atoms. The regioselectivity for the process of formation for the 2,6-isomer was also proved by theoretical calculations. Generally, in the experimental part, the simple and available approach for producing disubstituted carboxonium derivative was introduced, and the mechanism of this process was investigated with the help of theoretical calculations. The proposed approach can be applicable for the preparation of a wide range of disubstituted derivatives of closo-borate anions.