Purinyl N-directed aroylation of 6-arylpurine ribo- and 2'-deoxyribonucleosides, and mechanistic insights

The purinyl ring contains four embedded nitrogen atoms of varying basicities. Selective utilization of these ring nitrogen atoms can lead to relatively facile remote functionalization, yielding modified purinyl motifs that are otherwise not easily obtained. Herein, we report previously undescribed N-directed aroylation of 6-arylpurine ribo and the more labile 2'-deoxyribonucleosides. Kinetic isotope analysis as well as reaction with a well-defined dimeric, palladated 9-benzyl 6-arylpurine provided evidence for N-directed cyclometallation as a key step, with a plausible rate-limiting C-H bond cleavage. Radical inhibition experiments indicate the likely intermediacy of aroyl radicals. The chemistry surmounts difficulties often posed in the functionalization of polynitrogenated and polyoxygenated nucleosidic structures that possess complex reactivities and a labile glycosidic bond that is more sensitive in the 2'-deoxy substrates.

Covalent Modification of Nucleobases using Water-Soluble Palladium Catalysts

Nucleosides represent one of the key building blocks of biochemistry. There is significant interest in the synthesis of nucleoside-derived materials for applications as probes, biochemical models, and pharmaceuticals. Palladium-catalyzed cross-coupling reactions are effective methods for making covalent modification of carbon and nitrogen sites on nucleobases under mild conditions. Water-soluble catalysts derived from palladium and hydrophilic ligands, such as tris(3-sulfonatophenyl)phosphine trisodium (TPPTS), are efficient catalysts for a range of coupling reactions of unprotected halonucleosides. Over the past two decades, these methods have been extended to direct functionalization of halonucleotides, as well as RNA and DNA oligonucleotides (ONs) containing halogenated bases. These methods can be run under biocompatible conditions, including examples of Suzuki coupling of modified DNA in whole cells and tissue samples. In this account, development of this methodology by our group and others is highlighted along with the extension of these catalyst systems to modification of nucleotides and ONs.

Heteroatom-Assisted Regio- and Stereoselective Palladium-Catalyzed Carboxylation of 9-Allyl Adenine

Strategy for the synthesis of acyclic nucleoside analogs of biological relevance via highly regio- and stereoselective C-H functionalization employing heteroatom-assisted palladium-catalyzed carboxylation of 9-allyl adenine is disclosed. Substrate scope with different carboxylic acids was performed giving decent to good yields of the desired products. The method also allowed for the synthesis of deuterated analogs.

A Visible-Light-Promoted C-H Arylation and Heteroarylation of Uracil Derivatives with Diazoniums in Aqueous Conditions

The photoredox synthesis of C-5 (hetero)arylated uracil and uridine substrates with the corresponding diazonium salts is described. The coupling proceeds efficiently without protection of the hydroxyls at the ribose or pre-functionalization of the C5 position at the nucleobase. No transition-metal catalyst is used in this transformation, thereby avoiding metal contamination in the final products. The use of water as the medium also eliminates the impurities caused by the use of organic solvents. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of 5-aryl and 5-heteroaryl uracil derivatives Basic Protocol 2: Synthesis of 5-aryl uridine and deoxyuridine uridine derivatives.

Quadrol-Pd(II) complexes: phosphine-free precatalysts for the room-temperature Suzuki-Miyaura synthesis of nucleoside analogues in aqueous media

Commercially available Quadrol, N,N,N',N'-tetrakis(2-hydroxypropyl)ethylenediamine (THPEN), has been used for the first time as a N^N-donor neutral hydrophilic ligand in the synthesis and characterization of new water soluble palladium(II) complexes containing chloride, phthalimidate or saccharinate as co-ligands. [PdCl₂(THPEN)] (1) [Pd(phthal)₂(THPEN)] (2), [Pd(sacc)₂(THPEN)] (3) and the analogous complex with the closely related N,N,N',N'-tetrakis(2-hydroxyethyl)ethylenediamine (THEEN) [Pd(sacc)₂(THEEN)] (4) were efficiently prepared in a one-pot reaction from [PdCl₂(CH₃CN)₂] or Pd(OAc)₂. Structural characterization of 1 and 3 by single crystal X-ray diffraction produced the first structures reported to date of palladium complexes with Quadrol. The resultant palladium complexes are highly soluble in water and were found to be effective as phosphine-free catalysts for the synthesis of functionalized nucleoside analogues under room-temperature Suzuki-Miyaura cross-coupling conditions between 5-iodo-2'-deoxyuridine (& 5-iodo-2'-deoxycytidine) with different aryl boronic acids in neat water. This is the first report of the coupling process performed on nucleosides in water at room temperature.

Nickel-Catalyzed Hydroarylation Reaction: A Useful Tool in Organic Synthesis

This article describes the recent advances in the field of nickel-catalyzed hydroarylation reaction of alkenes, alkynes, and arenes. All reactions proceeded either through internal hydride transfer or in presence of...

Hydrogen Evolution Enabled Rhodaelectro-Catalyzed [4+2] Annulations of Purines and 7-Deazapurines with Alkynes

A rhodium-catalyzed electrochemical regioselective annulation of 6-phenylpurines and 6-phenyl-7-deazapurines with alkynes has been developed. Electricity is used to recycle the active rhodium-based catalyst, promote the evolution of H2 and help...

Aqueous and Visible-Light-Promoted C-H (Hetero)arylation of Uracil Derivatives with Diazoniums

Direct C5 (hetero)arylation of uracil and uridine substrates with (hetero)aryl diazonium salts under photoredox catalysis with blue light was reported. The coupling proceeds efficiently with diazonium salts and heterocycles in good functional group tolerance at room temperature in aqueous solution without transition-metal components. A plausible radical mechanism has been proposed.

Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides

Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.

Prospects and Applications of Palladium Nanoparticles in the Cross-coupling of (hetero)aryl Halides and Related Analogues

Discovering efficient methods for the formation of carbon-carbon bonds is a central ongoing theme in organic synthesis. Cross-coupling reactions catalysed by metal nanoparticles are attractive alternatives to the traditional use of metal counterparts due to the catalytic tunability, selectivity, recyclability and reusability of the nanoparticles. The ongoing search for sustainable processes demands that reusable and environmentally benign catalysts are used. While the advantages of nanoparticles catalysts over bulk catalysts cannot be overemphasised, the problem of sintering, agglomeration and leaching are drawbacks to their full industrial applications. Hence, efforts are being made towards advancing the efficiency of the catalytic nanoparticle systems over the years. This review presents the progress, the challenges and the prospects of palladium nanoparticle with focus on Heck, Suzuki, Hiyama and Sonogashira cross-coupling reactions involving (hetero) aryl halides and the analogues.

Photo-Induced Ruthenium-Catalyzed C-H Arylations at Ambient Temperature

Ambient temperature ruthenium-catalyzed C-H arylations were accomplished by visible light without additional photocatalysts. The robustness of the ruthenium-catalyzed C-H functionalization protocol was reflected by a broad range of sensitive functional groups and synthetically useful pyrazoles, triazoles and sensitive nucleosides and nucleotides, as well as multifold C-H functionalizations. Biscyclometalated ruthenium complexes were identified as the key intermediates in the photoredox ruthenium catalysis by detailed computational and experimental mechanistic analysis. Calculations suggested that the in situ formed photoactive ruthenium species preferably underwent an inner-sphere electron transfer.

Alkynylated and Dendronized 5-Aza-7-deazaguanine Nucleosides: Cross-Coupling with Tripropargylamine and Linear Alkynes, Click Functionalization, and Fluorescence of Pyrene Adducts†

The change of the recognition face of 5-aza-7-deazaguanine bridgehead nucleosides with respect to purine nucleosides permits the construction of new purine-purine or purine-pyrimidine base pairs in DNA and RNA. Clickable derivatives of 5-aza-7-deazaguanine were synthesized by introducing ethynyl, 1,7-octadiynyl, and tripropargylamino side chains in the 7-position of the 5-aza-7-deazapurine moiety by Sonogashira cross-coupling. Click reactions were performed with 1-azidomethylpyrene by the copper-catalyzed azide-alkyne cycloaddition. The copper(I)-catalyzed click reaction on the tripropargylamino nucleoside was significantly faster and higher yielding than that for nucleosides carrying linear alkynyl chains. Also, this reaction could be performed with copper(II) as the catalyst. An autocatalyzed cycle was suggested in which the click product acts as a catalyst. Pyrene click adducts of linear alkynylated nucleosides showed pyrene monomer emission, while tripropargylamino adducts showed monomer and excimer fluorescence. The fluorescence intensities of the 5-aza-7-deazaguanine nucleosides were higher than those of their 7-deazaguanine counterparts. The reported clickable nucleosides can be utilized to functionalize or to cross-link monomeric nucleosides or DNA for diagnostic or imaging purposes and other applications in nucleic acid chemistry and biotechnology.

Synthesis of 3-alkenylindoles through regioselective C-H alkenylation of indoles by a ruthenium nanocatalyst

3-Alkenylindoles are biologically and medicinally very important compounds, and their syntheses have received considerable attention. Herein, we report the synthesis of 3-alkenylindoles via a regioselective alkenylation of indoles, catalysed by a ruthenium nanocatalyst (RuNC). The reaction tolerates several electron-withdrawing and electron-donating groups on the indole moiety. Additionally, a "robustness screen" has also been employed to demonstrate the tolerance of several functional groups relevant to medicinal chemistry. With respect to the Ru nanocatalyst, it has been demonstrated that it is recoverable and recyclable up to four cycles. Also, the catalyst acts through a heterogeneous mechanism, which has been proven by various techniques, such as ICPMS and three-phase tests. The nature of the Ru nanocatalyst surface has also been thoroughly examined by various techniques, and it has been found that the oxides on the surface are responsible for the high catalytic efficiency of the Ru nanocatalyst.

A comprehensive overview of directing groups applied in metal-catalysed C-H functionalisation chemistry

The present review is devoted to summarizing the recent advances (2015-2017) in the field of metal-catalysed group-directed C-H functionalisation. In order to clearly showcase the molecular diversity that can now be accessed by means of directed C-H functionalisation, the whole is organized following the directing groups installed on a substrate. Its aim is to be a comprehensive reference work, where a specific directing group can be easily found, together with the transformations which have been carried out with it. Hence, the primary format of this review is schemes accompanied with a concise explanatory text, in which the directing groups are ordered in sections according to their chemical structure. The schemes feature typical substrates used, the products obtained as well as the required reaction conditions. Importantly, each example is commented on with respect to the most important positive features and drawbacks, on aspects such as selectivity, substrate scope, reaction conditions, directing group removal, and greenness. The targeted readership are both experts in the field of C-H functionalisation chemistry (to provide a comprehensive overview of the progress made in the last years) and, even more so, all organic chemists who want to introduce the C-H functionalisation way of thinking for a design of straightforward, efficient and step-economic synthetic routes towards molecules of interest to them. Accordingly, this review should be of particular interest also for scientists from industrial R&D sector. Hence, the overall goal of this review is to promote the application of C-H functionalisation reactions outside the research groups dedicated to method development and establishing it as a valuable reaction archetype in contemporary R&D, comparable to the role cross-coupling reactions play to date.

C-H Imidation of 7-Deazapurines

We developed and presented here a ferrocene-catalyzed C-H imidation of 7-deazapurines (pyrrolo[2,3-d]pyrimidines) with N-imidyl peroxyesters. The reactions occur regioselectively at position 8 in 7-deazapurines, leading to a series of 8-succinimido-, phtalimido-, or naphthalimido-7-deazapurine derivatives. Attempted hydrazinolysis of resulting 8-imidyl-7-deazapurines led to corresponding 8-amino-7-deazapurine, which was very unstable and quickly decomposed.

Rhodium(iii)-catalyzed CF3-carbenoid C–H functionalization of 6-arylpurines

An expedient route to access a new family of fluorine-containing purine derivatives via chelation-controlled rhodium(iii)-catalyzed carbenoid C–H functionalization has been developed.

Regioselective C–H and N–H functionalization of purine derivatives and analogues: a synthetic and mechanistic perspective

This perspective provides a systematic and concise overview of the recent development in C–H/N–H bond functionalization in purine derivatives and analogues.

Concise Xanthine Synthesis through a Double-Amidination Reaction of a 6-Chlorouracil with Amidines using Base-Metal Catalysis

A new and concise route towards xanthines through a double-amidination reaction is described; consecutive intermolecular C-Cl and intramolecular oxidative C-H amidination. N-uracil amidines are obtained through S_N AE on a 6-chlorouracil with amidines. Direct Cu-catalyzed oxidative C-H amidination on these N-uracil amidines yields polysubstituted xanthines. Sustainable oxidants, tBu₂ O₂ or O₂ , can be used in this oxidase-type reaction. The protocol allows for the introduction of N1, N3, N7, and C8 substituents during the xanthine-scaffold construction, thus avoiding post-functionalization steps. Both 6-chlorouracils and amidines are readily available commercially or through synthesis.

Ruthenium(II)-Catalyzed meta C-H Mono- and Difluoromethylations by Phosphine/Carboxylate Cooperation

Ruthenium(II)-catalyzed meta-selective C-H (di)fluoromethylation was accomplished by phosphine and carboxylate cooperation. The remote C-H functionalization was characterized by ample substrate scope, thereby setting the stage for meta-(di)fluoromethylation through facile C-H cleavage.

Synthesis of Cu-catalysed quinazolinones using a Csp3–H functionalisation/cyclisation strategy

A series of 2,3-disubstituted-4(3H)-quinazolinones were synthesised via a copper-catalysed C_sp3–H functionalisation/cyclisation of 2-amino-N,N-dialkylbenzamides.

Nickel-catalyzed C–H activation of purine bases with alkyl halides

C–H alkylations of purine nucleosides were achieved by means of user-friendly nickel catalysis with ample substrate scope and high levels of chemo, site and regio control, which among others enabled the direct fluorescent labeling of purines in terms of late stage diversification.

Visible-light-mediated oxidative demethylation of N6-methyl adenines

A novel solution for the chemical modulation of RNA epigenetics via biologically compatible photo-catalysis under visible light irradiation has been described.

Synthesis of 8-(1,2,3-triazol-1-yl)-7-deazapurine nucleosides by azide-alkyne click reactions and direct C-H bond functionalization

Treatment of toyocamycin or sangivamycin with 1,3-dibromo-5,5-dimethylhydantoin in MeOH (r.t./30 min) gave 8-bromotoyocamycin and 8-bromosangivamycin in good yields. Nucleophilic aromatic substitution of 8-bromotoyocamycin with sodium azide provided novel 8-azidotoyocamycin. Strain promoted click reactions of the latter with cyclooctynes resulted in the formation of the 1,2,3-triazole products. Iodine-mediated direct C8-H bond functionalization of tubercidin with benzotriazoles in the presence of tert-butyl hydroperoxide gave the corresponding 8-benzotriazolyltubercidin derivatives. The 8-(1,2,3-triazol-1-yl)-7-deazapurine derivatives showed moderate quantum yields and a large Stokes shifts of ~ 100 nm.

Ruthenium-Catalyzed C-H Bond Activation Approach to Azolyl Aminals and Hemiaminal Ethers, Mechanistic Evaluations, and Isomer Interconversion

C(sp³)-N bond-forming reactions between benzotriazole and 5,6-dimethylbenzotriazole with N-methylpyrrolidinone, tetrahydrofuran, tetrahydropyran, diethyl ether, 1,4-dioxane, and isochroman have been conducted using RuCl₃•3H₂O/t-BuOOH in 1,2-dichloroethane. In all cases, N1 and N2 alkylation products were obtained, and these are readily separated by chromatography. One of these products, 1-(isochroman-1-yl)-5,6-dimethyl-1H-benzotriazole, was examined by X-ray crystallography. It is the first such compound to be analyzed by this method, and notably, the benzotriazolyl moiety is quasi-axially disposed, consistent with the anomeric effect. This has plausible consequences, not observed previously. In contrast to other hemiaminal ether-forming reactions, which proceed via radicals, this Ru-catalyzed process is not suppressed in the presence of a radical inhibitor. Therefore, an oxoruthenium-species-mediated rapid formation of an oxocarbenium intermediate is believed to occur. In the radical-trapping experiment, previously unknown products containing both the benzotriazole and the TEMPO unit have been identified. In these products, it is likely that the benzotriazole is introduced via a Ru-catalyzed C-N bond formation, whereas C-O bond-formation with TEMPO occurs via a radical reaction. We show that reactions of THF with TEMPO are influenced by ambient light. A competitive reaction of THF and THF-d₈ with benzotriazole indicated that C-H bond cleavage occurs ca. 5 times faster than C-D cleavage. This is comparable to other metal-mediated radical reactions of THF, but lower than that observed for a reaction catalyzed by n-Bu₄N⁺I^-. Detailed mechanistic experiments and comparisons are described. The catalytic system was also evaluated for reactions of benzimidazole, imidazole, 1,2,4-triazole, and 1,2,3-triazole with THF, and successful reactions were achieved in each case. In the course of our studies, we discovered an unexpected but significant isomerization of some of the benzotriazolyl hemiaminal ethers. This is plausibly attributable to the pseudoaxial orientation of the heterocycle in the products and the stability of oxocarbenium ions, both of which can contribute to C-N bond cleavage and reformation. Predominantly, the N2-isomers rearrange to the N1-isomers even upon storage at low temperature! This previously unknown phenomenon has also been studied and described.

Cobalt(iii)-catalyzed C–H halogenation of 6-arylpurines: facile entry into arylated, sulfenylated and alkoxylated 6-arylpurines

Cp*Co(iii)-catalyzed C–H halogenation of 6-arylpurines has been reported under mild conditions and this protocol was further applied for the synthesis of arylated, sulfenylated and alkoxylated purine analogues.