Synthesis and ESR studies of nitronyl nitroxide-tethered oligodeoxynucleotides

Nitroxide radicals appended to phthalonitriles: synthesis, structural characterization and photophysical properties

The syntheses of 4-[4-(4,4,5,5-tetramethyl-2-imidazoline-3-oxide-1-oxyl-2-yl)phenoxy]phthalonitrile (3, C21H19N4O3) and 4-[4-(4,4,5,5-tetramethyl-2-imidazoline-1-oxyl-2-yl)phenoxy]phthalonitrile (4) were carried out by microwave-assisted nucleophilic aromatic substitution of 4-nitrophthalonitrile (2) by the pre-formed 2-(4-hydroxyphenyl)-4,4,5,5-tetramethyl-2-imidazoline-3-oxide-1-oxyl (1). Compounds 3 and 4 were characterized unambiguously by a rich array of analyses, such as melting point, FT–IR, MALDI–TOF MS, elemental analysis, UV–Vis, CV, EPR, magnetic measurements and single-crystal X-ray diffraction. Structural studies demonstrate that the C—H...X and C—X...π (X = O and N) interactions in the radical nitronyl nitroxide groups play an important role in the assembly of the crystal structures. Moreover, cyclic voltammetry analyses show that the phthalonitrile substituent retains the redox properties of the Ullman radicals.

Novel Carbazole-Based N-Heterocyclic Carbene Ligands to Access Synthetically Relevant Stilbenes in Pd-Catalyzed Coupling Processes

A series of new carbazole-based N-heterocyclic carbene (NHC) ligands have been synthesized in a simple and facile synthetic route and subsequently used in a Pd/carbazole-based NHC catalytic system, which was found to be effective in catalyzing Heck reactions to provide substituted stilbene derivatives in good yields. Several bioactive stilbenes, including pterostilbene, pinosylvin, trimethoxy resveratrol, and resveratrol, were synthesized in good yields, and a 10 mmol scale-up was also performed for trimethoxy resveratrol. The synthetic application was also extended by performing a double-tandem chemoselective Heck reaction followed by Miyaura borylation in a one-pot procedure to give single-step access to synthetically useful stilbenyl boronate esters. Similarly, a unique triple-tandem protocol of a chemoselective Heck reaction/Miyaura borylation/Suzuki-Miyaura coupling reaction sequence was performed for the one-pot modification of biologically relevant molecules.

Synthesis and Electron Paramagnetic Resonance Studies of Oligodeoxynucleotides Containing 2-N-tert-Butylaminoxyl-2'-deoxyadenosines

Oligodeoxynucleotides (ODNs) containing 2-N-tert-butylaminoxyl-2'-deoxyadenosine (A*) residues were synthesized to allow accurate monitoring of adenine motion by EPR spectroscopy through the agency of direct linkage of the acyclic aminoxyl group to the nucleobase, and EPR studies of the ODNs in single- and double-stranded forms were performed. Upon duplex formation, peak broadening and decreases in peak height were observed in EPR spectra, and the synthesized ODNs were shown to be excellent monitors of hybridization. Comparison of peak height and the h₁ /h₀ signal ratio provided information on the relative mobility of A* in duplexes with different stability. A second set of ODNs each containing two A* residues at different intervals and four dA residues were also synthesized. For these ODNs, correlations were observed between the EPR spectral shapes of the duplexes and the number of dA residues between A* residues, thus demonstrating the potential of A* residues in monitoring of the structures of nucleic acids.

Novel water-soluble phosphatriazenes: versatile ligands for Suzuki–Miyaura, Sonogashira and Heck reactions of nucleosides

Two new water-soluble phosphatriazene as versatile ligands for catalyzing Suzuki–Miyaura reactions of purines and pyrimidines in neat water with the possibility of recycling. Copper-free Sonogashira and Heck reaction were also made possible.

Palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides

Synthetic modification of nucleoside structures provides access to molecules of interest as pharmaceuticals, biochemical probes, and models to study diseases. Covalent modification of the purine and pyrimidine bases is an important strategy for the synthesis of these adducts. Palladium-catalyzed cross-coupling is a powerful method to attach groups to the base heterocycles through the formation of new carbon-carbon and carbon-heteroatom bonds. In this review, approaches to palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides are reviewed. Polar reaction media, such as water or polar aprotic solvents, allow reactions to be performed directly on the hydrophilic nucleosides and nucleotides without the need to use protecting groups. Homogeneous aqueous-phase coupling reactions catalyzed by palladium complexes of water-soluble ligands provide a general approach to the synthesis of modified nucleosides, nucleotides, and oligonucleotides.

Palladium-catalyzed Suzuki reaction in aqueous solvents applied to unprotected nucleosides and nucleotides

Nucleoside analogues have attracted much attention due to their potential biological activities.

Efficient synthesis of unprotected C-5-aryl/heteroaryl-2'-deoxyuridine via a Suzuki-Miyaura reaction in aqueous media

Following our previous results on an environmentally benign one-pot Sonogashira-cyclization protocol to obtain substituted furopyrimidine nucleosides under aqueous conditions, we investigate herein the Suzuki-Miyaura cross-coupling reactions of aryl and heteroaryl derivatives at the C5 position of unprotected 2'-deoxyuridine in the same media with a common catalyst system avoiding exotic ligands, since palladium acetate and triphenylphosphine afforded the expected products in moderate to good yields.

Synthesis of new, base-modified PNA monomers

A number of N-Boc-protected peptide nucleic acids (PNA) monomers containing 5-aryl- and 5-alkynyl-uracil bases have been synthesized using different palladium-catalyzed cross-coupling reactions. Starting from the base-unprotected 5-iodo-uracil PNA monomer, only the Stille couplings were accomplished successfully, while Suzuki couplings with boronic acids containing the same aryl groups failed. During Sonogashira couplings with terminal alkynes, significant amounts of unrequired furano[2,3-d]pyrimidine by-products were formed. Protection of the lactam function by p-methoxybenzylation prevented the opportunity for intramolecular cyclization as well as formation of a negative charge on the 4-O atom, making it possible to reach almost quantitative yields at Sonogashira couplings and acceptable conversions in Suzuki reactions.

A guanine-substituted nitronyl nitroxide radical forming a one-dimensional ferromagnetic chain

A stable guanine-substituted nitronyl nitroxide radical 1 has been synthesized and characterized. The single-crystal structure analyses and magnetic susceptibility measurements exhibit a one-dimensional architecture of guanine base resulting from carbonyl-amino hydrogen bonds in the solid state, giving a 1D ferromagnetic chain of the radical moieties.

Synthesis and Structure of a Nucleoside with π-Conjugated Nitroxide Spin Label Forming a One-Dimensional Ferromagnetic Chain

Spin labeled 2'-deoxyuridine, in which a significant fraction of the spin density is delocalized from a nitroxide radical to the DNA base residue, was prepared as a crystalline solid, stable at ambient conditions. The crystal packing, which includes multiple hydrogen bonds, leads to one-dimensional chains of molecules with predominant intrachain ferromagnetic coupling and weaker interchain antiferromagnetic coupling.

Watson–Crick pairing of nucleobases functionalized with open-shell molecular entities in crystalline solids

A Watson-Crick type molecular complex of adenine and thymine bases substituted with the stable radical of nitronylnitroxide has been synthesized, which forms a double-chain spin system in the crystal.