Imine-Palladacycles as Phosphine-Free Precatalysts for Low-Temperature Suzuki–Miyaura Synthesis of Nucleoside Analogues in Aqueous Media

Linkage Isomers of Triangular Pd Metallacycles and Catalysis in Aqueous Suzuki Coupling Reaction

The water-soluble trinuclear Pd metallacycles [Pd(tmeda)(4-Spy)]3(X)3 (tmeda = tetramethylethylenediamine, X = OTf, 2; NO3, 3) were synthesized from the ambidentate ligand 4-pyridylthiolate (Spy-) and [Pd(tmeda)X2] in 80 and 70% yield, respectively. Two possible linkage isomers are found in solution (slow interconversion found in the NMR) and in the solid state. Density functional calculations showed that the energy of the isomer with a D3-symmetric arrangement of the SPy ligand and all Pd atoms having N∧NPdSN coordination is only 7 kcal/mol lower. When reacting [Pd(tmeda)(NO3)2] with 4,4'-biphenyldithiolate (S2bph2-), the tetranuclear [{Pd(tmeda)}4(μ-S2bph)2](NO3)4 (1) was formed. A new type of undecanuclear Pd cluster was separated as a minor product from an acetone solution of 2 in air. The new complexes represent the first examples of water-soluble Pd metallacycles constructed from a pyridine-thiolate ligand. They show catalytic activity with turnover numbers ranging from 9 to 420 in aqueous Suzuki cross-coupling reactions using phenyl boronic acid and a number of aryl halides. An optimized system gave a TON of 6,900,000 and a TOF of 492,857 h-1. The catalyst could be reused eight times, and the activity has been attributed to the formation of PdNPs.

Rapid plugged flow synthesis of nucleoside analogues via Suzuki-Miyaura coupling and heck Alkenylation of 5-Iodo-2'-deoxyuridine (or cytidine)

Nucleosides modification via conventional cross-coupling has been performed using different catalytic systems and found to take place via long reaction times. However, since the pandemic, nucleoside-based antivirals and vaccines have received widespread attention and the requirement for rapid modification and synthesis of these moieties has become a major objective for researchers. To address this challenge, we describe the development of a rapid flow-based cross-coupling synthesis protocol for a variety of C5-pyrimidine substituted nucleosides. The protocol allows for facile access to multiple nucleoside analogues in very good yields in a few minutes compared to conventional batch chemistry. To highlight the utility of our approach, the synthesis of an anti-HSV drug, BVDU was also achieved in an efficient manner using our new protocol.

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Supplementary Information

The online version contains supplementary material available at 10.1007/s41981-023-00265-1.

Water-Soluble Pd-Imidate Complexes as Versatile Catalysts for the Modification of Unprotected Halonucleosides

Modification of unprotected nucleosides has been attracting continuous interest, since these building blocks themselves and their phosphate-upgraded corresponding nucleotides have shown a plethora of uses in fields like biochemistry or pharmacy. Pd-catalyzed cross-coupling reactions, conducted in water or its mixtures with polar organic solvents, have frequently been the researchers' choice for the functionalization of the purine/pyrimidine base of the unprotected nucleosides. In this scenario, the availability of hydrophilic ligands and its water-soluble palladium complexes has markedly set the pace of the advances. The approach of our group to the synthesis of such complexes, Pd-imidates specifically, has faced critical stages, namely the jump to synthesize water soluble complexes from our experience working in conventional solvents, the preparation of phosphine free complexes and the overall goal of getting catalytic systems able to work close to room temperature. The continuous feedback with Kapdi's group, experienced in the chemistry of nucleosides, has produced over the last decade the interesting results in both fields presented here.

Suzuki-Miyaura Coupling, Heck Alkenylation, and Amidation of DMTr-Protected 5-Iodo-2'-Deoxyuridine via Palladium-catalyzed Reactions

Modification of nucleosides via cross-coupling processes has been carried out extensively on unprotected halonucleosides to produce functionalized nucleosides that are often developed for incorporation into oligonucleotides or used as fluorescent probes. This approach requires protection of the 5'-OH with the 4,4'-dimethoxytrityl (DMTr) group, which is complicated and a common cause of reaction failure. Here we report a method for direct functionalization of 5'-O-DMTr-5-iodo-2'-deoxyuridine via Suzuki-Miyaura cross-coupling, Heck alkenylation, and carboamidation. This approach facilitates rapid synthesis of a variety of C5-substituted 5'-O-DMTr-2'-deoxyuridine derivatives. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of the SerrKap palladacycle complex Basic Protocol 2: Suzuki-Miyaura coupling of 5'-O-DMTr-5-iodo-2'-deoxyuridine using SerrKap palladacycle Basic Protocol 3: Heck coupling of 5'-O-DMTr-5-iodo-2'-deoxyuridine using SerrKap palladacycle Basic Protocol 4: Heck coupling of 5'-O-DMTr-5-iodo-2'-deoxyuridine with Ruth linker using Pd(OAc)₂ /PTABS Basic Protocol 5: Carbonylative amidation of 5'-O-DMTr-5-iodo-2'-deoxyuridine using Pd(OAc)₂ /PTABS.

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.