SNAr Reaction Research Articles

SNAr Regioselectivity Predictions: Machine Learning Triggering DFT Reaction Modeling through Statistical Threshold.

Fast and accurate prospective predictions of regioselectivity can significantly reduce the time and resources spent on unproductive transformations in the pharmaceutical industry. Density functional theory (DFT) reaction modeling through transition state theory (TST) and machine learning (ML) methods has been widely used to predict reaction outcomes such as selectivity. However, TST reaction modeling and ML methods are either time-consuming or data-dependent. Herein, we introduce a prototype seamlessly bridging ML and TST modeling by triggering resource-intensive but much less domain-sensitive DFT calculations only on less confident ML predictions. The proposed workflow was trained and tested on both the Pfizer internal dataset and the USPTO public dataset to predict regioselectivity for SNAr reactions. Our method is accurate and fast, which achieves 96.3 and 94.7% accuracy in predicting the correct major product on Pfizer and USPTO datasets, respectively, in a fraction of conventional TST computing time.

Exploration of intramolecular charge transfer in para-substituted nitrobenzofurazan: Experimental and theoretical analyses

The present work aims at exploring the high electrophilic character of 4-chloro-7-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl) toward the morpholine group by an SNAr reaction in acetonitrile or water (thereafter referred to as NBD-Morph). The electron-donating ability of the morpholine causes intra-molecular charge transfer (ICT). In this report, we present a comprehensive study on the optical characteristics using UV–Vis, photoluminescence (cw-PL) and its time-resolved (TR-PL) to determine the properties of the emissive intramolecular charge transfer (ICT) in the NBD-Morph donor–acceptor system. An exhaustive theoretical investigation utilizing the density functional theory (DFT) and its extension TD-DFT methods is an essential complement of experiments to rationalize and understand the molecular structure and related properties. The findings from QTAIM, ELF, and RDG analyses establish that the bonding between morpholine and NBD moieties is of the electrostatic or hydrogen bond type. In addition, the Hirshfeld surfaces have been established to explore the types of interactions. Further, the non-linear optical (NLO) responses of the compound have been examined. The structure–property relationships obtained through the combined experimental and theoretical offer valuable insights for designing efficient NLO material.

Synthesis of Thieno[3,2-d]pyrimidine Derivatives through Sequential SN Ar and Suzuki Reactions as Selective h-NTPDase Inhibitors.

In this study various of thieno[3,2-d]pyrimidine derivatives have been synthesized by treating different secondary amines through aromatic nucleophilic substitution reaction (SN Ar) followed by Suzuki reaction with aryl and heteroaryl boronic acids. A bis-Suzuki coupling was also performed to generate bis-aryl thienopyrimidine derivatives. The synthesized compounds were screened for the hydrolytic activity of h-NTPdase1, h-NTPdase2, h-NTPdase3, and h-NTPdase8. The compound N-benzyl-N-methyl-7-phenylthieno[3,2-d]pyrimidin-4-amine 3 j selectively inhibits the activity of h-NTPdase1 with IC50 value of 0.62±0.02 μM whereas, the compound 4 d was the most potent inhibitor of h-NTPdase2 with sub-micromolar IC50 value of 0.33±0.09 μM. Similarly, compounds 4 c and 3 b were found to be selective inhibitors for isozymes h-NTPdase3 (IC50 =0.13±0.06 μM) and h-NTPdase8 (IC50 =0.32±0.10 μM), respectively. The molecular docking study of the compounds with the highest potency and selectivity revealed the interactions with the important amino acid residues.

Photophysical and nonlinear optical properties of para-substituted nitrobenzofurazan: A comprehensive DFT investigation

We investigate the ability of the 4-chloro-7-nitrobenzofurazan (NBD-Cl) to append Pyrrolidine (Pyrr), a secondary amine, acting as a nucleophile group in SNAr reactions resulting in the fluorescent NBD-Pyrr compound. Their electrochemical and photo-physical responses have been thoroughly investigated using Cyclic Voltammetry (CV), UV–Visible, photoluminescence (cw-PL) and time resolved photoluminescence (TR-PL) spectroscopies. The intra-molecular charge transfer associated to nonlinear optical (NLO) properties of NBD-Pyrr molecule has reported, for the first time. Important NLO parameters such as dipole moment (μ), polarizability (α), anisotropy of polarizability (Δα) and first and second order hyperpolarizabilities (β and γ) are calculated at the B3LYP/6–31 + g(d,p) level of theory as well. Additionally, natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM), Hirshfeld surface (HS), Electron Localization Function (ELF), and Localized orbital locator (LOL) analyses have been used to illustrate structure and bonding in the NBD-Pyrr molecule.

Synthesis and photophysical properties of subphthalocyanine substituted with tetraphenylethylene moieties

Tetraphenylethylene-substituted phthalonitriles and corresponding subphthalocyanines have been synthesized. Mono- and di-substituted phthalonitriles could be prepared by a typical [Formula: see text]Ar reaction. The crystallographic structures of phthalonitriles indicated that intermolecular [Formula: see text]-[Formula: see text] interactions were suppressed by the bulky tetraphenylethylene moieties. Subphthalocyanines substituted with tetraphenylethylenes at peripheral and axial positions were obtained by boron-templated macrocyclization of phthalonitriles. Phthalonitriles showed typical aggregation-induced-emission behavior in THF/water mixed solvents, while fluorescence intensities of subphthalocyanines were decreased with increasing water content.

Shape‐ and Size‐Tunable Synthesis of Covalent Organic Cages through Rh‐Catalyzed Regioselective [2+2+2] Cycloaddition

AbstractCovalent organic cages have potential applications in molecular inclusion/recognition and porous organic crystals. Bridging arene units with sp3 atoms enables facile construction of rigid isolated internal vacancies, and various prismatic arene cages have been synthesized by kinetically controlled covalent bond formation. However, the synthesis of a tetrahedral one, which requires twice as much bond formation as prismatic ones, has been limited to a thermodynamically controlled dynamic SNAr reaction, and this reversible covalent bond formation made the resulting cage product chemically unstable. Here we report the Rh‐catalyzed high‐yielding and highly 1,3,5‐selective room temperature [2+2+2] cycloaddition of push‐pull alkynes and its application to the synthesis of chemically stable aryl ether cages of various shapes and sizes, including prismatic and tetrahedral forms. These aryl ether cages are highly crystalline and intertwine with each other to form regular packing structures. Some aryl ether cages encapsulated isolated water molecules in their hydrophobic cavity by hydrogen bonding with the multiple ester moieties.

Shape- and Size-Tunable Synthesis of Covalent Organic Cages through Rh-Catalyzed Regioselective [2+2+2] Cycloaddition.

Covalent organic cages have potential applications in molecular inclusion/recognition and porous organic crystals. Bridging arene units with sp3 atoms enables facile construction of rigid isolated internal vacancies, and various prismatic arene cages have been synthesized by kinetically controlled covalent bond formation. However, the synthesis of a tetrahedral one, which requires twice as much bond formation as prismatic ones, has been limited to a thermodynamically controlled dynamic SN Ar reaction, and this reversible covalent bond formation made the resulting cage product chemically unstable. Here we report the Rh-catalyzed high-yielding and highly 1,3,5-selective room temperature [2+2+2] cycloaddition of push-pull alkynes and its application to the synthesis of chemically stable aryl ether cages of various shapes and sizes, including prismatic and tetrahedral forms. These aryl ether cages are highly crystalline and intertwine with each other to form regular packing structures. Some aryl ether cages encapsulated isolated water molecules in their hydrophobic cavity by hydrogen bonding with the multiple ester moieties.

2-(3-Bromophenyl)imidazo[2,1-b]oxazole

The microwave-assisted reaction of 2-nitroimidazole with 3-bromophenacyl bromide in the presence of potassium carbonate as a base and dimethylformamide as a solvent afforded 2-(3-bromophenyl)imidazo[2,1-b]oxazole. The formation of this compound was explained via a domino mechanism comprising an initial N-alkylation reaction of the imidazole substrate, followed by the base-promoted deprotonation of the position adjacent to the carbonyl to give an enolate anion that finally cyclizes via an intramolecular SNAr reaction, with the loss of the nitro group as potassium nitrite. Then, the proposed 1-(3-bromophenacyl)-2-nitroimidazole intermediate could be isolated by reducing the reaction time and was shown to be a precursor of the imidazo[2,1-b]oxazole final product.

Transition-metal-free synthesis of 2-arylphenol via SNAr reaction of dibenzothiophene dioxide with KOH

Transition-metal-free synthesis of 2-arylphenol via SNAr reaction of dibenzothiophene dioxide with KOH

Synthesis, radiolabeling, and evaluation of a (4-quinolinoyl)glycyl-2-cyanopyrrolidine analogue for fibroblast activation protein (FAP) PET imaging.

Fibroblast activation protein (FAP) is regarded as a promising target for the diagnosis and treatment of tumors as it was overexpressed in cancer-associated fibroblasts. FAP inhibitors bearing a quinoline scaffold have been proven to show high affinity against FAP in vitro and in vivo, and the scaffold has been radio-labeled for the imaging and treatment of FAP-positive tumors. However, currently available FAP imaging agents both contain chelator groups to enable radio-metal labeling, making those tracers more hydrophilic and not suitable for the imaging of lesions in the brain. Herein, we report the synthesis, radio-labeling, and evaluation of a 18F-labeled quinoline analogue ([18F]3) as a potential FAP-targeted PET tracer, which holds the potential to be blood-brain barrier-permeable. [18F]3 was obtained by one-step radio-synthesis via a copper-mediated SNAR reaction from a corresponding boronic ester precursor. [18F]3 showed moderate lipophilicity with a log D 7.4 value of 1.11. In cell experiments, [18F]3 showed selective accumulation in A549-FAP and U87 cell lines and can be effectively blocked by the pre-treatment of a cold reference standard. Biodistribution studies indicated that [18F]3 was mainly excreted by hepatic clearance and urinary excretion, and it may be due to its moderate lipophilicity. In vivo PET imaging studies indicated [18F]3 showed selective accumulation in FAP-positive tumors, and specific binding was confirmed by blocking studies. However, low brain uptake was observed in biodistribution and PET imaging studies. Although our preliminary data indicated that [18F]3 holds the potential to be developed as a blood-brain barrier penetrable FAP-targeted PET tracer, its low brain uptake limits its application in the detection of brain lesions. Herein, we report the synthesis and evaluation of [18F]3 as a novel small-molecule FAPI-targeted PET tracer, and our results suggest further structural optimizations would be needed to develop a BBB-permeable PET tracer with this scaffold.

Chemo‐ and Regioselective Construction of Functionalized Isocoumarin, Flavone, and Isoquinolinedione via a One‐pot Reaction of o‐Quinol Acetate and Soft Nucleophiles

AbstractA one‐pot strategy for the synthesis of substituted isocoumarin, flavone, and isoquinolinedione derivatives through a switchable C‐arylation/lactonization or SNAr reaction from a wide range of soft nucleophiles and o‐quinol acetates has been developed. This base‐mediated protocol proceeds under transition‐metal‐free conditions and selectively affords various heteroarenes in 13–98% yields from readily prepared or commercially available 1,3‐dicarbonyl and α‐EWG‐substituted carbonyl compounds. The synthetic utility is further demonstrated in the synthesis of potential anti‐HIV and anti‐coronavirus derivatives and COX‐2 inhibitors. In addition, detailed experimental and computational studies are performed to provide an intensive understanding and strong support of the reaction mechanism.

N1‐Methylthiomethylation of (8‐Aza)6‐Chloropurine with DMSO through the Pummerer Rearrangement

AbstractN1‐[(Methylthio)methyl] hypoxanthines and aza hypoxanthines were efficiently prepared from 6‐chloropurines/azapurines and DMSO under microwave irradiation. DMSO was employed as a readily available and atom‐economic methylthiomethylating reagent and solvent without any other activator. The mechanistic investigations demonstrate that the reaction proceeded via sequential SNAr reaction and the Pummerer rearrangement. The current protocol provides an effective strategy for the synthesis of various N1‐[(methylthio)methyl] (8‐aza)hypoxanthines.

Synthesis of Adagrasib (MRTX849), a Covalent KRASG12C Inhibitor Drug for the Treatment of Cancer

A concise, transition-metal and protection-free synthesis of adagrasib (MRTX849), a novel KRASG12C inhibitor drug recently approved by the FDA, is reported. Introduction of two chiral building blocks to the tetrahydropyridopyrimidine core was accomplished via two sequential SNAr reactions. Extensive reaction optimization led to a robust, transition-metal-free oxidation of the sulfide intermediate. A judicious choice of the leaving group with favorable steric and electronic characteristics at the 4-OH position of the tetrahydropyridopyrimidine core enabled a facile SNAr displacement to introduce the chiral piperazine. This new, five-step, chromatography-free synthesis of adagrasib from readily available starting materials obviated the palladium catalysis and protecting group manipulations in the current commercial route and significantly improved the efficiency of the process in 45% overall yield.

An Efficient Undergraduate Synthesis of the Exorbitantly Priced Lambert–Eaton Myasthenic Syndrome Drug Amifampridine

An efficient synthesis of the exorbitantly priced Lambert–Eaton myasthenic syndrome drug amifampridine was developed and applied in the second-semester undergraduate organic chemistry laboratory. The two-step synthesis entails a nucleophilic aromatic substitution reaction of commercial 4-chloro-3-nitropyridine with methanolic ammonia to afford 4-amino-3-nitropyridine. Subsequent palladium-catalyzed nitro reduction provides amifampridine in high yield and purity. Amifampridine can alternatively be prepared by advanced undergraduate students in four linear steps beginning with 4-hydroxypyridine. Nitration of 4-hydroxypyridine to 4-hydroxy-3-nitropyridine and subsequent treatment with phosphoryl chloride provides the intermediate 4-chloro-3-nitropyridine, which is then subjected to the SNAr and reduction reactions to cleanly afford amifampridine without the need for column chromatography.

Reaction of Diaryliodonium Salts with Potassium Alkyl Xanthates as an Entry Point to Accessing Organosulfur Compounds.

Preparation of S-aryl xanthates via transition-metal-catalyzed or SNAr reactions is complicated by their further transformations under the utilized conditions. In contrast, S-arylation of potassium O-alkyl xanthates with diaryliodonium salts proceeds under mild conditions, enabling access to substituted S-aryl xanthates. The method exhibits good functional group tolerance and can be applied to the late-stage C-H functionalization of drug molecules. Divergent transformations of the resulting S-aryl xanthates provide rapid access to a range of medicinal chemistry-relevant organosulfur compounds.

Design, synthesis, anticancer and in silico assessment of 8-piperazinyl caffeinyl-triazolylmethyl hybrid conjugates.

In this paper, we have assessed the design, synthesis, characterization, anticancer properties, toxicity, and in silico study of 8-piperazinyl caffeinyl-triazolylmethyl derivatives as new caffeine hybrid conjugates. These compounds consist of four moieties comprising 8-caffeinyl, piperazinyl, 1,2,3-triazolyl, and alkyl substituents. The synthesis of these compounds was started by bromination of caffeine to attain 8-BC, SNAr reaction with piperazine to acquire 8-PC, N-propargylation of 8-PC and finally click Huisgen cycloaddition with diverse alkyl azides. These compounds were in vitro tested against two significant cancer cell lines comprising breast cancer MCF-7 (ATCC HTB-22) and melanoma cancer A-375 (ATCC CRL-1619) cell lines and activities compared with methotrexate (MTX) as a reference drug. Anticancer assessments indicated 12j (IC50 = 323 ± 2.6) and 12k (IC50 = 175 ± 3.2) were the most potent compounds against A-375 and MCF-7 cell growth, respectively and their activities were even stronger than MTX (IC50 = 418 ± 2 for A375 and IC50 = 343 ± 3.6 for MCF-7). Toxicities were determined by screening compounds against normal cell line HEK-293 (ATCC CRL-11268) and indicated that except 12i (IC50 = 371 ± 2.3), 12j (IC50 = 418 ± 2.4), and MTX (IC50 = 199 ± 2.4), all compounds are non-toxic. Docking was conducted for 12j and 12k and determined the strong binding affinities to B-RAF kinase and hDHFR enzymes, respectively. In silico pharmacokinetic and physiochemical profiles of tested compounds were investigated which indicated that most compounds obeyed Lipinski's rule of five (RO5). The DFT study on M06-2X/6-311G (d,p) was used to indicate HOMO, LUMO, MEP, and other parameters for a better understanding of 12j and 12k reactivity. Owing to anticancer properties, toxicity, and in silico data, 12j and 12k can be proposed for further research in the future.

Ortho-Lithiation driven one-pot synthesis of quinazolines via [2 + 2 + 2] cascade annulation of halofluorobenzenes with nitriles.

A one-pot synthesis of 2,4-disubstituted quinazoline derivatives from halofluorobenzenes with nitriles was reported, via sequential nucleophilic addition and SNAr reaction. The advantages of the present approach are transition metal free, easy to operate, and all the starting materials are commercially available.

Tetrahomo corona[4]arene-based spirophanes: synthesis, structure, and properties.

In contrast to a plethora of macrocyclic and cage compounds, spirophanes have remained largely unexplored. We report herein the construction, structure and properties of unprecedented tetrahomo corona[4]arene-based ditopic and tritopic macrocycles of spiro structures. Synthesis was conveniently achieved by means of an efficient SNAr reaction from simple and commercially available starting materials. Racemic samples were resolved into enantiopure chiral tetrahomo i-corona[4]arenes, spirophanes and bispirophanes which show interesting chiroptical properties. The acquired electron-deficient macrocyclic compounds were found to adopt unique conformational structures and to form distinct complexes with TTF in the solid state. Our study provides a new opportunity to develop multitopic macrocycles of different topologies which have potential applications in supramolecular chemistry.

Base-promoted tandem synthesis of 2-azaaryl indoline.

A novel tandem method to synthesize 2-azaaryl indoline promoted by LiN(SiMe3)2 from 2-azaaryl methyl amine and 2-fluoro benzyl bromides was developed. Mechanistic investigation indicated that this tandem cyclization was initiated by selective benzyl C-SN2 substitution followed by an intramolecular SNAr reaction. Diverse 2-azaaryl indoles could also be obtained via simple functional transformations.

Transition-metal-free synthesis of functional 2-arylphenols by an intermolecular SNAr reaction between dibenzofurans and various nucleophiles

Shown herein for the first time is the utilization of dibenzofurans for an SNAr reaction with various nucleophiles, including primary and secondary alcohols, aliphatic amines and phosphines.