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Synthesis of 8,1′-ethano-2′-deoxyinosine-containing oligonucleotides, and their antiparallel Watson–Crick and parallel Hoogsteen duplex-forming abilities

IF 2.1 3区化学 Q2 CHEMISTRY, ORGANIC

Tetrahedron

Pub Date : 2025-02-14 DOI: 10.1016/j.tet.2025.134538

Honoka Hanashiro, Yuta Ito, Yasufumi Fuchi, Yoshiyuki Hari

Recently, we developed oligonucleotides (ONs) containing syn-constrained 8,1′-ethano-2′-deoxyadenosine. In this study, we further explored the synthesis of 8,1′-ethano-2′-deoxyguanosine (ethano-dG) and 8,1′-ethano-2′-deoxyinosine (ethano-dI). Although ethano-dG could not be synthesized, ethano-dI, in which the inosine (^ethI) base was fixed in syn conformation, was successfully synthesized and incorporated into ONs. Subsequently, duplex-forming ability of ethano-dI-containing ONs was evaluated using ultraviolet (UV) melting experiments. Antiparallel Watson–Crick duplex containing the ^ethI:guanine base pair showed higher thermal stability than those containing other ^ethI:X base pairs (X = adenine, cytosine, or thymine) due to the formation of two Hoogsteen-type hydrogen bonds between ^ethI and guanine base at the Watson–Crick side. Although parallel Hoogsteen duplex formation generally requires acidic conditions, ethano-dI-containing ONs formed a parallel Hoogsteen duplex with the complementary DNA under neutral conditions, indicating that ^ethI stably recognized the cytosine base via two Watson–Crick-type hydrogen bonds. Overall, our findings suggest ethano-dI as a useful material to elucidate the biological functions of syn-oriented purine nucleosides in DNA.

{"title":"Synthesis of 8,1′-ethano-2′-deoxyinosine-containing oligonucleotides, and their antiparallel Watson–Crick and parallel Hoogsteen duplex-forming abilities","authors":"Honoka Hanashiro, Yuta Ito, Yasufumi Fuchi, Yoshiyuki Hari","doi":"10.1016/j.tet.2025.134538","DOIUrl":"10.1016/j.tet.2025.134538","url":null,"abstract":"<div><div>Recently, we developed oligonucleotides (ONs) containing <em>syn</em>-constrained 8,1′-ethano-2′-deoxyadenosine. In this study, we further explored the synthesis of 8,1′-ethano-2′-deoxyguanosine (ethano-dG) and 8,1′-ethano-2′-deoxyinosine (ethano-dI). Although ethano-dG could not be synthesized, ethano-dI, in which the inosine (<sup>eth</sup>I) base was fixed in <em>syn</em> conformation, was successfully synthesized and incorporated into ONs. Subsequently, duplex-forming ability of ethano-dI-containing ONs was evaluated using ultraviolet (UV) melting experiments. Antiparallel Watson–Crick duplex containing the <sup>eth</sup>I:guanine base pair showed higher thermal stability than those containing other <sup>eth</sup>I:X base pairs (X = adenine, cytosine, or thymine) due to the formation of two Hoogsteen-type hydrogen bonds between <sup>eth</sup>I and guanine base at the Watson–Crick side. Although parallel Hoogsteen duplex formation generally requires acidic conditions, ethano-dI-containing ONs formed a parallel Hoogsteen duplex with the complementary DNA under neutral conditions, indicating that <sup>eth</sup>I stably recognized the cytosine base via two Watson–Crick-type hydrogen bonds. Overall, our findings suggest ethano-dI as a useful material to elucidate the biological functions of <em>syn</em>-oriented purine nucleosides in DNA.</div></div>","PeriodicalId":437,"journal":{"name":"Tetrahedron","volume":"175 ","pages":"Article 134538"},"PeriodicalIF":2.1,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143437308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Sulfonyl-stabilized 4-alkylidene dihydropyridines as C-donor ligands in organotransition metal catalysis: Synthesis of palladium complexes

IF 2.1 3区化学 Q2 CHEMISTRY, ORGANIC

Tetrahedron

Pub Date : 2025-02-14 DOI: 10.1016/j.tet.2025.134540

Anushree Poddar , F. Christopher Pigge

Three palladium(II) complexes supported by new neutral η¹-C-donor ligands derived from alkylidene dihydropyridine derivatives are reported. The ligand frameworks are easily constructed from simple 4-alkylpyridines. The ligands feature peripheral aryl sulfonyl groups that increase acidity of picolyl C–H bonds, facilitate subsequent generation of relatively stable alkylidene dihydropyridines, and provide sites for attachment of additional metal ligating groups. Sulfonyl-stabilized alkylidene dihydropyridines readily coordinate PdCl₂ through the picolyl carbon in monodentate fashion or as C,N-chelating ligands when 2-pyridylsulfonyl groups are present. All complexes are air-stable and X-ray crystal structures of two complexes are reported. One Pd(II) complex was screened for catalytic activity and found to be moderately effective in mediating Suzuki cross-coupling reactions.

引用次数: 0

Photoinduced ligand-to-copper charge transfer for decarboxylative hydrogenation of aromatic carboxylic acids

IF 2.1 3区化学 Q2 CHEMISTRY, ORGANIC

Tetrahedron

Pub Date : 2025-02-13 DOI: 10.1016/j.tet.2025.134536

Zhengjia Shen , Jiani Wei , Xue Hu , Zimu Gu , Qiqi Shao , Xuan Chen , Mingming Wang , Dongliang Zhang

A novel ligand-to-metal charge transfer (LMCT)-based synthetic methodology is presented for the decarboxylative hydrogenation of aromatic carboxylic acids. This approach features mild reaction conditions, economical copper-mediated catalysis, and exceptional functional group tolerance. The study addresses significant challenges in aromatic carboxylic acid transformations and underscores the potential of photochemical copper catalysis in contemporary organic synthesis.

引用次数: 0

Unusual transformation of 4-hydroxy-6-methyl-3-nitro-2H-pyrano[3,2-c]quinoline-2,5(6H)-dione into 1-methyl-4-substituted amino-2-oxo-1,2-dihydroquinoline-3-carboxylic acids

IF 2.1 3区化学 Q2 CHEMISTRY, ORGANIC

Tetrahedron

Pub Date : 2025-02-11 DOI: 10.1016/j.tet.2025.134532

Al-Shimaa Badran, Magdy A. Ibrahim, Mai A. Mostafa

Reaction of 4-hydroxy-6-methyl-3-nitro-2H-pyrano[3,2-c]quinoline-2,5(6H)-dione (1) with some primary amines namely methylamine, ethylamine, propylamine, n-butylamine, benzylamine and furfurylamine in molar ratio 1:2, in boiling DMF afforded the unexpected 1-methyl-4-substitutedamino-2-oxo-1,2-dihydroquinoline-3-carboxylic acids. The suggested mechanism was typically described. Structures of the synthesized were clearly confirmed using spectroscopic and elemental analysis.

引用次数: 0

Synthesis of new hybrid compounds of imidazo[1,2-a]pyrimidine/pyridine based on quinoxaline through palladium-catalyzed coupling reactions and heteroannulation

IF 2.1 3区化学 Q2 CHEMISTRY, ORGANIC

Tetrahedron

Pub Date : 2025-02-08 DOI: 10.1016/j.tet.2025.134521

Marzieh Enjilzadeh, Ali Keivanloo, Mohammad Bakherad

New hybrid compounds, including imidazo[1,2-a]pyrimidin-2-yl(3-(substituted)quinoxalin-2-yl)methanone and its imidazo[1,2-a]pyridine analogs, have been successfully prepared via palladium-catalyzed reactions. The synthesis involved the reaction of 3-substituted-2-chloroquinoxalines with 2-amino-1-(prop-2-yn-1-yl)pyrimidinium/pyridinium bromide under optimized reaction conditions. These conditions included Pd(PPh₃)₂Cl₂ (5 mol %), CuI (10 mol%) in the presence of Et₃N in DMF at 70 °C, resulting in the formation of the desired hybrid compounds. Furthermore, imidazo[1,2-a]pyridine hybrid compounds were synthesized through one-pot multicomponent reactions of 2,3-dicholoroquinoxaline, 2-amino-1-(prop-2-yn-1-yl)pyridinium bromide, primary and secondary amines, under optimized conditions. These processes provided efficient protocols to synthesize novel imidazo[1,2-a]pyrimidine/pyridine based on quinoxaline through palladium-catalyzed reaction with high yields. A one-pot reaction, high reaction yields, energy efficiency, and a straightforward reaction process are significant advantages of this protocol.

{"title":"Synthesis of new hybrid compounds of imidazo[1,2-a]pyrimidine/pyridine based on quinoxaline through palladium-catalyzed coupling reactions and heteroannulation","authors":"Marzieh Enjilzadeh, Ali Keivanloo, Mohammad Bakherad","doi":"10.1016/j.tet.2025.134521","DOIUrl":"10.1016/j.tet.2025.134521","url":null,"abstract":"<div><div>New hybrid compounds, including imidazo[1,2-<em>a</em>]pyrimidin-2-yl(3-(substituted)quinoxalin-2-yl)methanone and its imidazo[1,2-<em>a</em>]pyridine analogs, have been successfully prepared via palladium-catalyzed reactions. The synthesis involved the reaction of 3-substituted-2-chloroquinoxalines with 2-amino-1-(prop-2-yn-1-yl)pyrimidinium/pyridinium bromide under optimized reaction conditions. These conditions included Pd(PPh<sub>3</sub>)<sub>2</sub>Cl<sub>2</sub> (5 mol %), CuI (10 mol%) in the presence of Et<sub>3</sub>N in DMF at 70 °C, resulting in the formation of the desired hybrid compounds. Furthermore, imidazo[1,2-<em>a</em>]pyridine hybrid compounds were synthesized through one-pot multicomponent reactions of 2,3-dicholoroquinoxaline, 2-amino-1-(prop-2-yn-1-yl)pyridinium bromide, primary and secondary amines, under optimized conditions. These processes provided efficient protocols to synthesize novel imidazo[1,2-<em>a</em>]pyrimidine/pyridine based on quinoxaline through palladium-catalyzed reaction with high yields. A one-pot reaction, high reaction yields, energy efficiency, and a straightforward reaction process are significant advantages of this protocol.</div></div>","PeriodicalId":437,"journal":{"name":"Tetrahedron","volume":"175 ","pages":"Article 134521"},"PeriodicalIF":2.1,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143387428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Synthesis and photophysics of color-pure blue emitters featuring oxaboraphenanthrene as a novel structural motif

IF 2.1 3区化学 Q2 CHEMISTRY, ORGANIC

Tetrahedron

Pub Date : 2025-02-08 DOI: 10.1016/j.tet.2025.134522

Sunwu Song , Siyang Feng , Liangxuan Wang , Begoña Milián-Medina , Reinhold Wannemacher , Johannes Gierschner , Min Sang Kwon

In a recent study, we synthesized novel, color-pure blue emitters, based on a simple ‘pencil and paper’ concept, termed DOBFT and DOBFIT, inspired by our ‘Poly-Heteroaromatic Omni-Delocalization’ (PHOD) concept. The molecules' asymmetric structure, distinct from the DABNA framework, posed significant synthetic challenges, necessitating careful modification of existing strategies and considerable trial and error. While previous publications have primarily focused on the PHOD concept and the properties of DOBFT and DOBFIT, they often overlooked the complexities of their synthesis. In this paper, we provide a detailed account of the synthesis processes and challenges, offering valuable insights for researchers pursuing similar efforts. Additionally, we introduce a new molecule, DOBFITX, with its synthesis meticulously documented, along with a comprehensive, combined spectroscopic and computational analysis of the photophysical properties of these molecules.

引用次数: 0

Ligand-induced transformation to cyclic conformation of trimers of porphyrin dendrimer analogs

IF 2.1 3区化学 Q2 CHEMISTRY, ORGANIC

Tetrahedron

Pub Date : 2025-02-07 DOI: 10.1016/j.tet.2025.134523

Takumi Nakao , Yoshimitsu Tachi , Masatoshi Kozaki

Three zinc porphyrin dendrimer analogs with rigid conjugated backbones were synthesized and connected via a copper-catalyzed Hüisgen 1,3-dipolar cycloaddition reaction to form a trimer with two flexible linkages. Comparison of the ¹H NMR and UV–vis absorption spectra of the trimer with those of the corresponding monomers indicated that the trimer adopted an extended conformation in chloroform. The addition of a Y-shaped ligand with three pyridyl terminals to a chloroform solution of the trimer resulted in the formation of a 1:1 complex between the trimer and ligand. A binding constant of K = 2.7 × 10⁶ M⁻¹ was estimated by UV–vis titration. The characteristic up-field shift of the signals for pyridine protons was observed in the ¹H NMR spectrum of the 1:1 mixture of the trimer and ligand. Theoretical calculations suggested that coordination of pyridyl terminals to three zinc porphyrin cores led to the trimer adopting a cyclic conformation.

引用次数: 0

One pot synthesis of coumarin fused fluorescein derivative for mercury ion detection: An experimental and theoretical approach

IF 2.1 3区化学 Q2 CHEMISTRY, ORGANIC

Tetrahedron

Pub Date : 2025-02-05 DOI: 10.1016/j.tet.2025.134518

Praveenakumara A. Valmiki , Lohit Naik , M.S. Thippeswamy , C.V. Maridevarmath , Arun K. Shetter , Amnah Mohammed Alsuhaibani , Moamen S. Refat , G.H. Malimath

In this study, a highly fluorescent fluorescein-based derivative (2FLC) was synthesized using a one-pot synthesis method. The structure of the molecule was confirmed through physicochemical analysis, including ¹H NMR, FT-IR, and mass spectroscopy. The chemosensor property of 2FLC with different metal ions (Cu ²⁺, Al³⁺, Ag ⁺, Hg²⁺, Mg²⁺, Fe²⁺, Co²⁺, K⁺, Zn²⁺, Ni²⁺, Pb²⁺, Cd²⁺ and Mn²⁺) is investigated through absorption and fluorescence studies in a water medium. Interestingly, it is observed that the 2FLC exhibited a remarkable turn-off fluorescence response upon adding Hg²⁺ ion as compared to different metal ions. Further, competitive metal ion studies indicate that the receptor 2FLC exhibits exceptional selectivity in detecting Hg²⁺ ion without being affected by other metal ions. The detection limit of 2FLC for targeted Hg²⁺ ion was 8.87 μM. The binding stoichiometry between the receptor 2FLC and the Hg²⁺ metal ion was verified using both Job's plot and the Benasi-Hildbrand methods and found to be 1:1. Theoretical studies and FT-IR spectra confirmed the strong binding and formation of 2FLC-Hg²⁺ complex. Overall, the results suggest that the newly synthesized water-soluble 2FLC molecule may be used as a chemosensor to detect Hg²⁺ ion.

{"title":"One pot synthesis of coumarin fused fluorescein derivative for mercury ion detection: An experimental and theoretical approach","authors":"Praveenakumara A. Valmiki , Lohit Naik , M.S. Thippeswamy , C.V. Maridevarmath , Arun K. Shetter , Amnah Mohammed Alsuhaibani , Moamen S. Refat , G.H. Malimath","doi":"10.1016/j.tet.2025.134518","DOIUrl":"10.1016/j.tet.2025.134518","url":null,"abstract":"<div><div>In this study, a highly fluorescent fluorescein-based derivative (2FLC) was synthesized using a one-pot synthesis method. The structure of the molecule was confirmed through physicochemical analysis, including <sup>1</sup>H NMR, FT-IR, and mass spectroscopy. The chemosensor property of 2FLC with different metal ions (Cu <sup>2+</sup>, Al<sup>3+</sup>, Ag <sup>+</sup>, Hg<sup>2+</sup>, Mg<sup>2+</sup>, Fe<sup>2+</sup>, Co<sup>2+</sup>, K<sup>+</sup>, Zn<sup>2+</sup>, Ni<sup>2+</sup>, Pb<sup>2+</sup>, Cd<sup>2+</sup> and Mn<sup>2+</sup>) is investigated through absorption and fluorescence studies in a water medium. Interestingly, it is observed that the 2FLC exhibited a remarkable turn-off fluorescence response upon adding Hg<sup>2+</sup> ion as compared to different metal ions. Further, competitive metal ion studies indicate that the receptor 2FLC exhibits exceptional selectivity in detecting Hg<sup>2+</sup> ion without being affected by other metal ions. The detection limit of 2FLC for targeted Hg<sup>2+</sup> ion was 8.87 μM. The binding stoichiometry between the receptor 2FLC and the Hg<sup>2+</sup> metal ion was verified using both Job's plot and the Benasi-Hildbrand methods and found to be 1:1. Theoretical studies and FT-IR spectra confirmed the strong binding and formation of 2FLC-Hg<sup>2+</sup> complex. Overall, the results suggest that the newly synthesized water-soluble 2FLC molecule may be used as a chemosensor to detect Hg<sup>2+</sup> ion.</div></div>","PeriodicalId":437,"journal":{"name":"Tetrahedron","volume":"175 ","pages":"Article 134518"},"PeriodicalIF":2.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143387429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Click synthesis via 1,3-dipolar addition- A versatile route to tetrazine derivatives and In silico corroboration as anti-muscular dystrophy agent

IF 2.1 3区化学 Q2 CHEMISTRY, ORGANIC

Tetrahedron

Pub Date : 2025-02-04 DOI: 10.1016/j.tet.2025.134520

Satheeshkumar Nagaraj, Karpagam Ezhilarasan, Rajalakshmi Ramarajan

Click chemistry, celebrated for its efficiency and selectivity, has emerged as a powerful tool for the rapid synthesis of tetrazines. This study introduces a novel approach to accessing tetrazines from symmetrical azines and sodium azide, facilitating the streamlined construction of these versatile compounds. Renowned for their exceptional stability and reactivity, tetrazines are highly coveted in diverse fields including materials science, medicinal chemistry, and imaging. The newly synthesized tetrazine derivatives were rigorously characterized using a suite of spectroscopic techniques, including IR, ¹H and ¹³C NMR, 2D NMR, and mass spectrometry. To assess their reactivity and stability, the energy gap (ΔE) was computed using density functional theory. Furthermore, in silico molecular docking studies were performed against the muscular dystrophy protein 2VD5 to explore its potential biological activity. This innovative synthetic strategy provides a robust platform for the expeditious development of a diverse array of tetrazine-based compounds with promising applications across various scientific domains.

{"title":"Click synthesis via 1,3-dipolar addition- A versatile route to tetrazine derivatives and In silico corroboration as anti-muscular dystrophy agent","authors":"Satheeshkumar Nagaraj, Karpagam Ezhilarasan, Rajalakshmi Ramarajan","doi":"10.1016/j.tet.2025.134520","DOIUrl":"10.1016/j.tet.2025.134520","url":null,"abstract":"<div><div>Click chemistry, celebrated for its efficiency and selectivity, has emerged as a powerful tool for the rapid synthesis of tetrazines. This study introduces a novel approach to accessing tetrazines from symmetrical azines and sodium azide, facilitating the streamlined construction of these versatile compounds. Renowned for their exceptional stability and reactivity, tetrazines are highly coveted in diverse fields including materials science, medicinal chemistry, and imaging. The newly synthesized tetrazine derivatives were rigorously characterized using a suite of spectroscopic techniques, including IR, <sup>1</sup>H and <sup>13</sup>C NMR, 2D NMR, and mass spectrometry. To assess their reactivity and stability, the energy gap (ΔE) was computed using density functional theory. Furthermore, in silico molecular docking studies were performed against the muscular dystrophy protein 2VD5 to explore its potential biological activity. This innovative synthetic strategy provides a robust platform for the expeditious development of a diverse array of tetrazine-based compounds with promising applications across various scientific domains.</div></div>","PeriodicalId":437,"journal":{"name":"Tetrahedron","volume":"175 ","pages":"Article 134520"},"PeriodicalIF":2.1,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143349082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The application of azoarenes in the synthesis of nitrogen-containing heterocycles

IF 2.1 3区化学 Q2 CHEMISTRY, ORGANIC

Tetrahedron

Pub Date : 2025-02-01 DOI: 10.1016/j.tet.2024.134428

Azim Ziyaei Halimehjani, Nima Sadeghzadeh, Sina Moghaddam

Azoarenes are efficient intermediates in synthetic organic chemistry. In this review, the application of azoarenes for the synthesis of nitrogen-containing heterocyles including pyrroles, benzotriazoles, triazolidines, indoles, indazoles, oxindoles, quinolines and its reduced derivatives, phenazines, hydropyridazinones, cinnolines, benzimidazoles and other useful N-containing heterocycles are reviewed and discussed. For this purpose, the reaction of azoarenes with various organic small molecules such as alkenes, alkynes, azides, NO₂ gas, nitroso, amino acids, azomethine ylides, canbonyl compounds, diazoesteres, sulfoxonium ylides, tosyl hydrazines, allyl halides, and many other reagents were investigated under metal/transition-metal catalysts, photocatalysts, or electrochemical conditions to afford the target heterocycles with at least one nitrogen atom. In this review, around 70 papers are summarized and discussed during the years 2000–2024.

偶氮烯类是合成有机化学中的高效中间体。本综述回顾并讨论了偶氮烯在合成含氮杂环方面的应用，包括吡咯、苯并三唑、三唑烷、吲哚、吲哚、氧吲哚、喹啉及其还原衍生物、吩嗪、哒嗪酮、噌啉、苯并咪唑和其他有用的含 N 杂环。为此，在金属/过渡金属催化剂、光催化剂或电化学条件下，研究了偶氮烯与各种有机小分子（如烯烃、炔烃、叠氮化物、NO2 气体、亚硝基、氨基酸、偶氮甲基酰化物、羰基化合物、重氮酯、亚砜酰化物、对甲苯基肼、烯丙基卤化物和许多其他试剂）的反应，从而得到至少含有一个氮原子的目标杂环。本综述对 2000-2024 年间约 70 篇论文进行了总结和讨论。

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