Fluorescent 7-Deazapurine Derivatives from 5-Iodocytosine via a Tandem Cross-Coupling-Annulation Reaction with Terminal Alkynes

Abstract

Fluorescent bicyclic analogs of cytosine have been ­synthesized directly from derivatives of 5-iodocytosine by a one-pot sequential Sonogashira cross-coupling and annulation with terminal alkynes. The spectral properties of these compounds depend on the identity of the alkyne. 7-Deazapurines synthesized from ­substituted phenylacetylenes possess greater fluorescence than those derived from alkyl substituted alkynes.

Key words

annulation - cross-coupling - nucleobase - pyrrolocytosine - peptide nucleic acid

References

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1

Current address: Department of Chemistry, 80 St. George Street, University of Toronto, Toronto, ON, M5S 3H6, Canada.

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Typical Procedure for Cross-Coupling without Cyclization:
Compound 1 (1.0 mmol) was suspended in dry, deoxygenated DMF (7 mL) to which CuI (0.2 mmol), Et₃N (2.0 mmol), alkyne (3.0 mmol) and Pd(PPh₃)₄ (0.1 mmol) were sequentially added. The reaction mixtures were stirred in the dark at r.t. for 24 h and products were isolated by precipitation in EtOAc or by flash chromatography. All NMR spectra were obtained at 400.1 MHz (¹H) or 100.6 MHz (¹³C) in d ₆-DMSO. Compound 3a: white solid, mp 211-213 °C (dec). ¹H NMR: δ = 8.06 (s, 1 H), 7.77 (s, 1 H), 7.38-7.33 (m, 5 H), 6.98 (s, 1 H), 5.16 (s, 2 H), 4.54 (s, 2 H), 4.28 (s, 2 H), 3.28 (s, 3 H). ¹³C NMR: δ = 168.4, 160.1, 154.6, 142.0, 137.9, 108.2, 99.3, 66.4, 61.0, 57.4, 51.9, 14.0. HRMS: m/z calcd for C₁₇H₁₇N₃O₄: 327.1219; found: 327.1217. Compound 3b: white solid, mp 205-214 °C (dec). ¹H NMR: δ = 7.94 (s, 1 H), 7.72 (s, 1 H), 7.39-7.31 (m, 5 H), 6.79 (s, 1 H), 5.16 (s, 2 H), 4.54 (s, 2 H), 2.39 (t, J = 6.9 Hz, 2 H), 1.54-1.47 (m, 2 H), 1.39-1.30 (m, 2 H), 1.27-1.26 (m, 4 H), 0.85 (t, J = 5.8 Hz, 3 H). ¹³C NMR: δ = 168.4, 165.1, 154.2, 148.9, 135.7, 128.4, 128.1, 127.9, 95.8, 90.1, 71.5, 66.2, 49.9, 30.8, 28.1, 28.0, 22.0, 19.0, 14.0. HRMS: m/z calcd for C₂₁H₂₅N₃O₃: 367.1896; found: 367.1888. Compound 3c: off-white solid, mp 214-216 °C (dec). ¹H NMR: δ = 8.11 (s, 1 H), 7.82 (s, 1 H), 7.37-7.32 (m, 5 H), 6.72 (s, 1 H), 5.16 (s, 2 H), 4.54 (s, 2 H), 0.20 (s, 9 H). ¹³C NMR: δ = 168.3, 164.6, 153.9, 150.8, 135.6, 128.5, 128.2, 127.9, 99.7, 96.4, 89.3, 66.3, 50.0, -0.1. HRMS: m/z calcd for C₁₈H₂₁N₃O₃Si: 355.1352; found: 355.1360. Compound 3d: beige solid, mp 235 °C (dec). ¹H NMR: δ = 8.18 (s, 1 H), 7.85 (s, 1 H), 7.60-7.58 (m, 2 H), 7.42-7.31 (m, 8 H), 7.14 (s, 1 H), 5.18 (s, 2 H), 4.60 (s, 2 H). ¹³C NMR: δ = 168.3, 164.5, 154.1, 150.2, 135.7, 131.4, 131.2, 128.5, 128.5, 127.9, 122.4, 93.9, 89.2, 81.1, 66.3, 50.1. HRMS: m/z calcd for C₂₁H₁₇N₃O₃: 359.1270; found: 359.1281.

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Typical Procedure for the Heteroannulation Reaction:
Compound 3 (1.0 mmol) was dissolved in dry, deoxygenated DMF (7 mL) to which CuI (0.2 mmol), Et₃N (2.0 mmol), alkyne (3.0 mmol) and Pd(PPh₃)₄ (0.1 mmol) were sequentially added. The reaction mixtures were stirred in the dark at 50 °C for 24 h after which the solvent was removed under vacuum. The reaction mixture was redissolved in absolute EtOH and refluxed for 18 h. All products were isolated by silica gel column chromatography. All NMR spectra were obtained at 400.1 MHz (¹H) or 100.6 MHz (¹³C) in d ₆-DMSO. Compound 4a: pale yellow solid, mp 205-207 °C (dec). ¹H NMR: δ = 11.37 (1 H, br s), 8.39 (1 H, s), 6.22 (1 H, s), 4.69 (2 H, s), 4.33 (2 H, s), 4.13 (2 H, q, J = 7.1 Hz), 3.26 (3 H, s), 1.19 (3 H, t, J = 7.2 Hz). ¹³C NMR: δ = 168.4, 141.9, 137.9, 108.6, 99.4, 66.4, 61.0, 57.4, 14.0. HRMS: m/z calcd for C₁₂H₁₅N₃O₄: 265.1063; found: 265.1057. Compound 4b: pale yellow solid, mp 134-139 °C. ¹H NMR: δ = 11.15 (1 H, s), 8.24 (1 H, s), 5.93 (1 H, s), 4.67 (2 H, s), 4.12 (2 H, q, J = 7.1 Hz), 1.16 (16 H, overlapping signals). HRMS: m/z calcd for C₁₆H₂₃N₃O₃: 305.17394; found: 305.17383. Compound 4c: pale yellow solid, mp 211-218 °C (dec). ¹H NMR: δ = 11.24 (1 H, s), 8.46 (1 H, s), 6.46 (1 H, s), 4.71 (2 H, s), 4.13 (2 H, q, J = 7.1 Hz), 1.19 (3 H, t, J = 7.2 Hz), 0.25 (9 H, s). HRMS: m/z calcd for C₁₃H₁₉N₃O₃Si: 293.1196; found: 293.1197. Compound 4d: green solid, mp 335-338 °C (dec). ¹H NMR: δ = 11.83 (1 H, br s), 8.46 (1 H, s), 7.83 (2 H, d, J = 7.4 Hz), 7.44 (2 H, t, J = 7.7 Hz), 7.34 (1 H, t, J = 7.5 Hz), 6.78 (1 H, s), 4.72 (2 H, s), 4.14 (2 H, q, J = 7.1 Hz), 1.20 (3 H, t, J = 7.1 Hz). HRMS: m/z calcd for C₁₆H₁₅N₃O₃: 297.1113; found: 297.1119. Compound 4e: yellow solid, mp 279-284 °C (dec). ¹H NMR: δ = 11.74 (1 H, s), 8.38 (1 H, s), 7.77 (2 H, d, J = 6.9 Hz), 7.00 (2 H, d, J = 6.9 Hz), 6.62 (1 H, s), 4.71 (2 H, s), 4.14 (2 H, q, J = 7.1 Hz), 3.79 (3 H, s), 1.20 (3 H, t, J = 7.1 Hz). HRMS: m/z calcd for C₁₇H₁₇N₃O₄: 327.1219; found: 327.1223. Compound 4f: orange solid, mp 280-285 °C (dec). ¹H NMR: δ = 12.08 (1 H, br s), 8.63 (1 H, s), 8.28 (2 H, d, J = 9.0 Hz), 8.09 (2 H, d, J = 8.8 Hz), 7.13 (1 H, s), 4.75 (2 H, s), 4.15 (2 H, q, J = 7.1 Hz), 1.21 (3 H, t, J = 7.1 Hz). HRMS: m/z calcd for C₁₆H₁₄N₄O₅: 342.0964; found: 342.0972. Compound 4g: yellow solid mp 154-158 °C (dec). ¹H NMR: δ = 11.61 (1 H, br s), 8.27 (1 H, s), 7.64 (2 H, d, J = 9.0 Hz), 6.74 (2 H, d, J = 9.0 Hz), 6.46 (1 H, s), 4.68 (2 H, s), 4.13 (2 H, q, J = 7.0 Hz), 2.94 (6 H, s), 1.20 (3 H, t, J = 7.0 Hz). LR ESI-TOF: m/e (%) = 381.1 (75) [K adduct], 325.0(100) [-CH₃], 268.9 (15), 147.1 (25); calcd for C₁₈H₂₀N₄O₃: 340.4. Compound 4h: red-brown solid, mp 136-141 °C. ¹H NMR: δ = 11.48 (1 H, br s), 8.27 (1 H, s), 6.28 (1 H, s), 4.85 (2 H, br t, J = 1.7 Hz), 4.68 (2 H, s), 4.38 (2 H, br t, J = 1.7 Hz), 4.14 (2 H, q, J = 7.1 Hz), 4.09 (5 H, s), 1.21 (3 H, t, J = 7.1 Hz). HRMS: m/z calcd for C₂₀H₁₉FeN₃O₃: 405.0775; found: 405.0768.

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The electron-rich substituted pyrroles 4e and 4g were markedly less stable than the parent phenyl-substituted (4d) or p-nitrophenyl substituted (4f) compounds. Whilst 4d and 4f are stable in solution for months, 4e (p-methoxy) slowly decomposed to non-fluorescent products over the same timeframe and 4g was isolated with difficulty.