Benzylic Position Research Articles

Development of hydrophobic tag purifying monophosphorylated RNA for chemical synthesis of capped mRNA and enzymatic synthesis of circular mRNA.

We developed phosphorylation reagents with a nitrobenzyl hydrophobic tag and used them for 5'-phosphorylation of chemically or transcriptionally synthesized RNA. The capability of hydrophobic tags to synthesize 5'-monophosphorylated RNA was evaluated based on the yield of the desired oligonucleotides, stability of protecting groups during cleavage/deprotection, separation ability in reverse-phase HPLC (RP-HPLC), and deprotection efficiency after RP-HPLC purification. The results showed that a nitrobenzyl derivative with a tert-butyl group at the benzyl position was most suitable for RNA 5'-phosphorylation. Using the developed phosphorylation reagent, we chemically synthesized 5'-phosphorylated RNA and confirmed that it could be purified by RP-HPLC and the following deprotection. In addition, we demonstrated complete chemical synthesis of minimal mRNA by chemical capping of 5'-monophosphorylated RNA. Ribonucleoside 5'-monophosphates with hydrophobic protecting groups have also been developed and used as substrates to transcriptionally synthesize 5'-phosphorylated RNA with>1000 bases. From the mixture of the by-products and the desired RNA, only 5'-monophosphorylated RNA could be effectively isolated by RP-HPLC. Furthermore, monophosphorylated RNA can be converted into circular mRNA via RNA ligase-mediated cyclization. Circular mRNA expression of nanoluciferase in cultured cells and mice. These techniques are important for the production of chemically synthesized mRNA and circular mRNA.

Site‐selective Photoredox‐Catalyzed Late‐stage Benzylic Hydrogen Isotope Exchange

A highly regioselective visible light photoredox‐catalyzed hydrogen isotope exchange (HIE) of benzylic positions in both simple and complex molecules is reported. The process follows a dual catalytic approach using an acridinium photocatalyst in combination with a thiol‐based hydrogen atom transfer catalyst, while the use of D2O as an isotope source ensures operational simplicity and cost‐effectiveness. High reactivity has been achieved for electron‐rich benzylic positions. Moreover, targeted radical formation enables unprecedented selective HIE on intramolecular competing benzylic and alpha to heteroatom positions with moderate to excellent deuterium incorporation. The utility of the reaction was demonstrated on the late‐stage HIE of several natural compounds and drug derivatives. Experimental studies and density functional theory (DFT) calculations suggested a single electron transfer (SET) mechanism followed by deprotonation to generate the benzylic radical, and revealed the importance of halogenated solvents or additives. Upon a weak complexation of the halogenated species to the substrate, an oxidation potential lowering effect is induced, as well as a stabilization of the radical‐cation species through spin delocalization.

Site-selective Photoredox-Catalyzed Late-stage Benzylic Hydrogen Isotope Exchange.

A highly regioselective visible light photoredox-catalyzed hydrogen isotope exchange (HIE) of benzylic positions in both simple and complex molecules is reported. The process follows a dual catalytic approach using an acridinium photocatalyst in combination with a thiol-based hydrogen atom transfer catalyst, while the use of D2O as an isotope source ensures operational simplicity and cost-effectiveness. High reactivity has been achieved for electron-rich benzylic positions. Moreover, targeted radical formation enables unprecedented selective HIE on intramolecular competing benzylic and alpha to heteroatom positions with moderate to excellent deuterium incorporation. The utility of the reaction was demonstrated on the late-stage HIE of several natural compounds and drug derivatives. Experimental studies and density functional theory (DFT) calculations suggested a single electron transfer (SET) mechanism followed by deprotonation to generate the benzylic radical, and revealed the importance of halogenated solvents or additives. Upon a weak complexation of the halogenated species to the substrate, an oxidation potential lowering effect is induced, as well as a stabilization of the radical-cation species through spin delocalization.

Catalyst-Controlled Strategies to Override the Bond Dissociation Energy-Driven Selectivity of Benzylic C(sp3)–H Insertions

AbstractCatalytic C(sp3)–H insertion reactions of arylalkanes generally proceed at the benzylic position as a consequence of the lower bond dissociation energy (BDE) of the corresponding C–H bond. This account gives a brief overview of recent studies aimed at designing catalyst-controlled amination reactions to go beyond this BDE-driven selectivity. They permit the selective conversion of neutral C–H bonds with a BDE greater than 95 kcal mol–1 for the formation of alkylamines.1 Introduction2 Catalyst-Controlled Site-Selective C–H Insertion Reactions3 Catalyst-Controlled Intermolecular Amination of Nonactivated C–H Bonds of Arylalkanes4 Conclusion

Photocatalytic Regioselective Redox-Neutral 1,3-Oxypyridylation of Aryl Cyclopropanes.

Pyridines and cyclopropanes are important structural units in chemistry. Herein, we introduce a photoredox-catalyzed approach for the ring opening and 1,3-oxypyridylation of aryl cyclopropanes using 4-cyanopyridines and carboxylic acids. This sequential process involves single-electron oxidation of the aryl cyclopropane, leading to nucleophilic ring opening and radical pyridylation at the benzylic position. The redox-neutral reaction exhibits high regioselectivity under mild reaction conditions, offering a broad substrate scope and wide applicability.

Reduction and Hydrocyanation of Aziridines with C−C Bond Cleavage

AbstractThe carbon‐carbon bond in three‐membered ring of 2,3‐diaryl aziridines was reductively cleaved to give the corresponding dibenzylamine derivatives by electrocyclic ring opening of N‐Li or N‐Na aziridines followed by reduction of the 2‐azaallyl anion formed with sodium borohydride in ethanol. Hydrocyanation of the 2‐azaallyl anion with trimethylsilyl cyanide gave a secondary amine bearing a cyano group at the benzylic position. The effects of substituents on the electrocyclic ring opening of N‐Li aziridines were also clarified.

Intramolecular Buchner Reaction: Experimental and Theoretical Comparison of the Effect of the Carbene Substituent on the Chemoselectivity

AbstractThe intramolecular Buchner reaction is a powerful transformation able to dearomatize benzenic rings. However, the competitive C−H insertion of the carbene moiety into benzylic positions still remains a limitation, and the reasons governing this uncomplete chemoselectivity are poorly understood. The carbene substitution, in particular, has been observed to influence the selectivity strongly, though the currently proposed explanation relying on the electrophilicity of the metallocarbene hardly describes some experimental results reported in the literature. In this article, we present our experimental observations of intramolecular rhodium‐catalyzed Buchner reactions, combined with DFT calculations on selected carbene substituents, to propose a complementary explanation for the observed chemoselectivity modification.

Metal-Free Switchable Chemo- and Regioselective Alkylation of Oxindoles Using Secondary Alcohols.

In this study, we have disclosed N-alkylation and C-alkylation reactions of 2-oxindoles with secondary alcohols. Interestingly, these chemoselective reactions are tunable by changing the reaction conditions. Utilization of protic solvent and Brønsted acid catalyst afforded C-alkylation, whereas, aprotic solvent and Lewis acid catalyst afforded N-alkylation of 2-oxindoles in good to excellent yields. Regioselectivity is achieved by protecting the N-center of the oxindole and C5 alkylated product is furnished exclusively. This protocol is notable because it demonstrates functionalization at the C7 position of oxindole without the need for any directing group at the N-center. Further, a new protocol has been reported for C-H oxygenation at the benzylic position of one of the C5 alkylated derivative.

Recent Advances in Direct Regioselective C-H Chlorination at Aromatic and Aliphatic.

Direct installation of key functionalities in a molecule through C-H bond activation is one of the thrust areas as well as challenging task in organic synthesis. Particularly, introduction of chlorine in a molecule imparts additional benefits for further functionalizations as well as improves the electronic behaviour such as lipophilicity and polarity towards drug development process. The chlorinated molecules have also been established as efficient biologically relevant scaffolds. Current manuscript has been focused on the direct installation of the chlorine atom at various aromatic and aliphatic positions to produce functional molecules. The key highlight of the manuscript belongs to the site selectivity (regioselectivity) for the installation of chlorine functionality. Manuscript describes the advanced methods developed for the direct C-H chlorination reactions and further simplified for the chlorination reactions at various positions including aromatic (o-, m-, and p-), benzylic, heteroaromatic, and aliphatic positions. Directing groups (DGs) and the coordination with the catalyst is the key for the enhancement of regioselectivities during direct C-H chlorination reactions.

Computational Insights into Palladium-Catalyzed Site-Selective Anilide and Benzamide-Type [3+2] Annulation via Double C-H Bond Activation.

The mechanism of palladium-catalyzed annulation reactions of benzamide- and anilide-type aromatic systems with maleimides is investigated using density functional theory. Double C-H bond activation is key to forming the desired annulation product. The first C-H bond activation for anilide- and amide-type ligands can occur at the ortho and benzylic C-H bonds, while the second C-H activation occurs at the meta carbon of the aromatic rings. For the anilide-type system, ortho and benzylic C-H bond activations occur via four- and five-membered palladacycles, respectively. In contrast, for the benzamide-type system, ortho and benzylic C-H bond activations occur via five- and six-membered palladacycles, respectively. The energy span model suggests that the initial C-H bond activation step at the benzylic position determines the turnover frequency for both anilide- and benzamide-type systems. Energy decomposition analysis and distortion-interaction/activation-strain analyses are employed to understand the electronic and steric factors controlling the turnover frequency-determining transition state.

Enhancing chloride/fluoride selectivity with hydrophobic side-chain anion exchange membranes in electrodialysis

The selective separation of chloride ions (Cl−) from fluoride ions (F−) is a critical concern in various industries due to the potential risks of F− on public health and industrial operations. However, Cl−/F− separation is known to be technologically challenging, considering they have the same charge and valency. This study explores the design of anion exchange membranes (AEMs) in electrodialysis to achieve Cl−/F− separation based on the difference in their hydration energy. Poly(2,6-dimethyl-1,4-phenylene oxide) (PPO) polymers brominated at varying reaction temperatures were employed as the basic AEM material, enabling fine-tuning of the hydrophobic properties of the resulting membranes through selective bromination at the benzyl or aryl positions and the subsequent quaternization with tertiary amines of different chain lengths, ultimately enhancing their selectivity. The developed AEMs are tested in electrodialysis involving a binary Cl−/F− mixture. The obtained membranes exhibited remarkable selectivity, reaching as high as 12.5 ± 1.0, surpassing the performance of commercial monovalent selective AEMs. The results demonstrate the potential of Cl−/F− separation by electrodialysis and highlight the significance of tailored membrane design in achieving the separation of ions with the same valency.

Palladium-Catalyzed Tsuji-Trost-Type Reaction of 3-Indolylmethylacetates with O, and S Soft Nucleophiles.

The chemical valorization of widespread molecules in renewable sources is a field of research widely investigated in the last decades. In this context, we envisaged that indole-3-carbinol, present in different Cruciferae plants, could be a readily available building block for the synthesis of various classes of indoles through a palladium-catalyzed Tsuji-Trost-type reaction with O and S soft nucleophiles. The regiochemical outcome of this high-yielding functionalization shows that the nucleophilic substitution occurs only at the benzylic position. Interestingly, with this protocol, the sulfonyl unit could be appended to the indole nucleus, providing convenient access to new classes of molecules with potential bioactivity.

Cobalt Catalyzed α-Hydroxylation of Arylacetic Acid Equivalents with Dioxygen.

A cobalt catalyst, under oxidative conditions, facilitates the single electron transfer process in N-pyridyl arylacetamides to form α-carbon-centered radicals that readily react with molecular oxygen, giving access to mandelic acid derivatives. In contrast to the known benzylic hydroxylation approaches, this approach enables chemo- and regioselective hydroxylation at a benzylic position adjacent to (N-pyridyl)amides. Mild conditions, broad scope, excellent selectivity, and wide synthetic practicality set up the merit of the reaction.

Metallaphotoredox deuteroalkylation utilizing thianthrenium salts

Deuterium labeling compounds play a crucial role in organic and pharmaceutical chemistry. The synthesis of such compounds typically involves deuterated building blocks, allowing for the incorporation of deuterium atoms and functional groups into a target molecule in a single step. Unfortunately, the limited availability of synthetic approaches to deuterated synthons has impeded progress in this field. Here, we present an approach utilizing alkyl-substituted thianthrenium salts that efficiently and selectively introduce deuterium at the α position of alkyl chains through a pH-dependent HIE process, using D2O as the deuterium source. The resulting α-deuterated alkyl thianthrenium salts, which bear two deuterium atoms, exhibit excellent selectivity and deuterium incorporation in electrophilic substitution reactions. Through in situ formation of isotopically labelled alkyl halides, these thianthrenium salts demonstrate excellent compatibility in a series of metallaphotoredox cross-electrophile coupling with (hetero)aryl, alkenyl, alkyl bromides, and other alkyl thianthrenium salts. Our technique allows for a wide range of substrates, high deuterium incorporation, and precise control over the site of deuterium insertion within a molecule such as the benzyl position, allylic position, or any alkyl chain in between, as well as neighboring heteroatoms. This makes it invaluable for synthesizing various deuterium-labeled compounds, especially those with pharmaceutical significance.

Selective Oxidations of Toluenes and Benzyl Alcohols by an Unspecific Peroxygenase (UPO)

Unspecific Peroxygenases (UPOs) have emerged as robust biocatalysts for selective oxygenation reactions, as they are easily produced at scale and require only hydrogen peroxide as the external oxidant. UPOs can catalyze the oxygenation of the primary benzylic carbons of toluenes to give alcohol, aldehyde and carboxylic acid products. They can also catalyze hydroxylation at the benzylic position of ethylbenzenes, and the subsequent oxidation of the secondary alcohols to ketones. In this study, we have investigated factors that affect the balance of products in UPO‐catalyzed benzylic oxygenations using a range of functionalised toluenes and ethyl benzenes, and a UPO from Agrocybe aegerita (rAaeUPO‐PaDa‐I‐H variant). The product distribution is dependent upon a mixture of steric and electronic effects and, in selected cases, controlling the reaction conditions permits products from each product series to be generated chemoselectively. In this way, electron poor toluenes were converted directly into carboxylic acids in isolated yields of 36–99% on preparative scale.

Neglected no longer: Selective C–H activation of the non-resonant C3 benzylic position of pyridine

Neglected no longer: Selective C–H activation of the non-resonant C3 benzylic position of pyridine

Predisposition in Dynamic Covalent Chemistry: The Role of Non-Covalent Interactions in the Assembly of Tetrahedral Boronate Cages.

Directional bonding strategies guide the design of complex molecular architectures, yet challenges arise due to emergent behavior. Rigid structures face geometric constraints and sensitivity to mismatches, hindering the efficient assembly of molecular organic cages (MOCs). Harnessing intramolecular non-covalent interactions offers a promising solution, broadening geometrical possibilities and enhancing adaptability to boost assembly yields. However, identifying these interactions remains challenging, with their full potential sometimes latent until final assembly. This study explores these challenges by synthesizing boronic acid tripods with varied oxygen positions at the tripodal feet and investigating their role in assembling tetrahedral boronate MOCs. Our results reveal substantial differences in the assembly efficiency among tripods. While the building blocks with oxygen in the benzylic position relative to the central aromatic ring form the MOCs in high yields, those with the oxygen atom directly bound to the central aromatic ring, only yield traces. Through X-ray crystallography and DFT analyses, we elucidate how intramolecular interactions profoundly influence the geometry of the building blocks and cages in a relay-like fashion, highlighting the importance of considering intramolecular interactions in the rational design of (supra)molecular architectures.

Design of sec-Benzyl Vinyl Ethers toward the Synthesis of Alternating Copolymers Composed of Vinyl Alcohol and Vinyl Ether Units.

In this work, we designed benzyl vinyl ethers carrying alkyl substituents at the benzyl position (i.e., sec-BnVEs) as bulky, reactive, and transformable monomers to realize the alternating cationic copolymerization with an alkyl vinyl ether (VE). In particular, the isopropyl substitution caused not only the bulkiness to suppress the successive propagation but also an enhancement of the vinyl group reactivity to promote crossover propagation with a less bulky VE comonomer. The isopropyl-substituted BnVE (iPr-BnVE) underwent living cationic alternating copolymerization with n-butyl VE (nBVE), and the alternating propagation was strongly suggested by the reactivity ratios. The subsequent deprotection of the sec-benzyl pendant afforded the vinyl alcohol (VA)-nBVE alternating copolymer, and the corresponding statistical copolymer was also synthesized by using the nonsubstituted monomer (BnVE) instead of iPr-BnVE. The alternating copolymer exhibited a higher glass transition temperature, which likely stems from the uniform and efficient hydrogen-bonding formation due to the periodic sequence.

Practical and efficient oxygenation of benzylic C-H bonds with dioxygen catalyzed by two-dimensional porous organic frameworks possessing porphyrin cobalt(II) units

Metalloporphyrin T(4-Br)PPCo was used in the construction of two-dimensional porous organic framework materials (2D POFs) in order to achieve the direct benzyl C-H bonds oxygenation. In order to prevent the disordered diffusion of free radicals in 2D POFs, a restricted reaction channel was constructed, and heterogeneous catalysis was applied to decrease the deep oxygenation of partial oxygenation products due to central metal sites. All 2D POFs were characterized as amorphous microporous materials containing highly and uniformly dispersed Co2+. It was used to partially oxygenate C-H bonds at benzyl position employing dioxygen in solvent-free condition, and the conversion and selectivity were improved at the same time, especially when residual -B(OH)2 and -Br were capped. Compared with T(4-Br)PPCo, the substrate conversion increased from 39 % to 66 %, and the selectivity for 4-nitroacetophenone increased from 66 % to 91 %. The reaction mechanism, apparent kinetics and substrate compatibility were also studied. In this work, it provided a guiding reference for the effective C-H bonds oxygenation and other free radical based chemical reactions. The use of POFs in catalytic chemistry was further broadened, and a successful method for improving the catalytic characteristics of POFs by capping the remaining active groups was suggested.

The Multifaceted Chemistry of [2.2]Paracyclophane‐Based Thioethers with Palladium(II) Complexes

AbstractThe reactions of planar chiral ([2.2]paracyclophan‐4‐yl)methyl thioethers ([2.2]PCP‐CH2‐SR) with various palladium(II) sources (PdL2) were studied. Unexpectedly, with most of the sulfur substrates investigated (SR=Ph, 2‐pyridyl, Me, n‐dodecyl), and independently of the PdL2 salt employed (L=TFA, OAc, OPiv, Cl, Br), loss of the SR sulfanyl unit, along with incorporation of one palladium L ligand to the lateral benzylic position of the [2.2]PCP core, has been observed. In contrast, the precursor featuring a t‐butylsulfanyl group (R=t‐Bu) exhibited a distinct reactivity. An ortho C(sp2)−H activation took place, and allowed the formation of a [2.2]paracyclophane‐based SC‐palladacycle, in an efficient and highly diastereoselective manner (83 % yield, single diastereoisomer).