Synlett 2021; 32(17): 1714-1718
DOI: 10.1055/a-1545-7086
letter

A Convenient Approach to meso-Uracil–4,4-Difluoro-4-bora-3a, 4a-diaza-s-indacene Derivatives

M. Trapani
a   CNR- ISMN Istituto per lo Studio dei Materiali Nanostrutturati, c/o Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche e Ambientali, 98166 V. le F. Stagno D’Alcontres 31, Messina, Italy
,
M. A. Castriciano
a   CNR- ISMN Istituto per lo Studio dei Materiali Nanostrutturati, c/o Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche e Ambientali, 98166 V. le F. Stagno D’Alcontres 31, Messina, Italy
,
J. A. A. W. Elemans
b   Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
,
A. Nicosia
c   Dipartimento di Scienze Chimiche, University of Catania, V. A. Doria 6, 95100 Catania, Italy
,
P. Mineo
c   Dipartimento di Scienze Chimiche, University of Catania, V. A. Doria 6, 95100 Catania, Italy
d   CNR-IPCF Istituto per i Processi Chimico-Fisici, V.le F. Stagno D’Alcontres 37, I-98158 Messina, Italy
,
M. Cordaro
e   Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche e Ambientali, 98166 V. le F. Stagno D’Alcontres 31, University of Messina, Messina, Italy
› Author Affiliations
The authors thank the MIUR (PRIN 2015 project no.2015XBZ5YA) and the MatISSE “Materiali Innovativi e Sostenibili per la Salute e l’Energia” (CUP G77B17000180009, grant to M.T.).


Abstract

An effective and convenient protocol for the synthesis of 1-substituted uracil-6-carbaldehyde derivatives has been developed. A three-step sequence permits the preparation of uracil-6-carbaldehydes with various substituents at the N-1 in large quantities by using low-cost precursors. The aldehyde-functionalized uracils served as useful precursors for the preparation of meso-(1-substituted 6-uracil)-derivatives of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY). In this way, regioselectively functionalized BODIPYs with a direct connection to a nucleobase were prepared in yields of 30–45%. MALDI-TOF mass spectrometry, NMR, UV/vis absorption, and steady-state and time-­resolved fluorescence spectroscopies were used to characterize the structures and the spectroscopic/photophysical properties of the resultant dyes.

Supporting Information



Publication History

Received: 06 June 2021

Accepted after revision: 07 July 2021

Accepted Manuscript online:
07 July 2021

Article published online:
18 August 2021

© 2021. Thieme. All rights reserved

Georg Thieme Verlag KG
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  • References and Notes

    • 1a Ashford DL, Gish MK, Vannucci AK, Brennaman MK, Templeton JL, Papanikolas JM, Meyer TJ. Chem. Rev. 2015; 115: 13006
    • 1b Gust D, Moore TA, Moore AL. Acc. Chem. Res. 2009; 42: 1890
    • 2a Loudet A, Burgess K. Chem. Rev. 2007; 107: 4891
    • 2b Ulrich G, Ziessel R, Harriman A. Angew. Chem. Int. Ed. 2008; 47: 1184
    • 2c Boens N, Leen V, Dehaen W. Chem. Soc. Rev. 2012; 41: 1130
    • 2d Bañuelos J. Chem. Rec. 2016; 16: 335
    • 2e Panniello A, Trapani M, Cordaro M, Dibenedetto CN, Tommasi R, Ingrosso C, Fanizza E, Grisorio R, Collini E, Agostiano A, Curri ML, Castriciano MA, Striccoli M. Chem. Eur. J. 2021; 27: 2371
    • 3a Chen Y, Wan L, Zhang D, Bian Y, Jian J. Photochem. Photobiol. Sci. 2011; 10: 1030
    • 3b Qin W, Baruah M, Van der Auweraer M, De Schryver FC, Boens N. J. Phys. Chem. A 2005; 109: 7371
    • 3c Fresch E, Peruffo N, Trapani M, Cordaro M, Bella G, Castriciano MA, Collini E. J. Chem. Phys. 2021; 154: 084201
    • 4a Bañuelos J, Arroyo-Córdoba IJ, Valois-Escamilla I, Alvarez-Hernández A, Peña-Cabrera E, Hu R, Tang BZ, Esnal I, Martíneza V, López Arbeloa I. RSC Adv. 2011; 1: 677
    • 4b Cordaro M, Mineo P, Nastasi F, Magazzù G. RSC Adv. 2014; 4: 43931
  • 5 Jiao L, Yu C, Wang J, Briggs EA, Besley NA, Robinson D, Ruedas-Rama MJ, Orte A, Crovetto L, Talavera EM, Alvarez-Pez JM, Van der Auweraer M, Boens N. RSC Adv. 2015; 5: 89375
  • 6 Sobenina LN, Vasil’tsov AM, Petrova OV, Petrushenko KB, Ushakov IA, Clavier G, Meallet-Renault R, Mikhaleva AI, Trofimov BA. Org. Lett. 2011; 13: 2524
    • 7a Meng Q, Kim DH, Bai X, Bi L, Turro NJ, Ju J. J. Org. Chem. 2006; 71: 3248
    • 7b Cornelius M, Wörth CG. T. C, Kliem H.-C, Wiessler M, Schmeiser HH. Electrophoresis 2005; 26: 2591
    • 7c Kurata S, Kanagawa T, Yamada K, Torimura M, Yokomaku T, Kamagata Y, Kurane R. Nucleic Acids Res. 2001; 29: e34
    • 7d Bi L, Kim DH, Ju J. J. Am. Chem. Soc. 2006; 128: 2542
    • 7e Deore PS, Soldatov DV, Manderville RA. Sci. Rep. 2018; 8: 16874
    • 7f Güixens-Gallardo P, Zawada Z, Matyašovský J, Dziuba D, Pohl R, Kraus T, Hocek M. Bioconjugate Chem. 2018; 29: 3906
  • 8 Prlj A, Fabrizio A, Corminboeuf C. Phys. Chem. Chem. Phys. 2016; 18: 32668
    • 9a Li F, Zhang Y, Zhou L, Zhang X, Chen Z. J. Porphyrins Phthalocyanines 2018; 22: 944
    • 9b Ehrenschwender T, Wagenknecht H.-A. Synthesis 2008; 3657
    • 9c Scala A, Cordaro M, Mazzaglia A, Risitano F, Venuti A, Sciortino MT, Grassi G. Mol. Diversity 2013; 17: 479
  • 10 Boens N, Verbelen B, Dehaen W. Eur. J. Org. Chem. 2015; 6577
  • 11 Shi X, Barkigia KM, Fajer J, Drain CM. J. Org. Chem. 2001; 66: 6513
  • 12 Holzhauser C, Wagenknecht H.-A. J. Org. Chem. 2013; 78: 7373
  • 13 Ahmed S, Lofthouse R, Shaw G. J. Chem. Soc., Chem. Commun. 1974; 959a
  • 14 Ahmed S, Lofthouse R, Shaw G. J. Chem. Soc., Perkin Trans. 1 1976; 1969
  • 15 Patra D, Ramesh M, Sahu D, Padhy H, Chu C.-W, Wei K.-H, Lin H.-C. Polymer 2012; 53: 1219
  • 16 Tanaka H, Hayakawa H, Miyasaka T. Tetrahedron 1982; 38: 2635
  • 17 1-Butyluracil-6-carbaldehyde (3a) 1-Butyl-6-methyluracil (2a; 200 mg, 1 mmol) and SeO2 (113 mg, 1 mmol) were dissolved in 10% HOAc–1,4-dioxane (10 mL), and the mixture was stirred at 100 °C for 3 h. The product was purified by column chromatography (silica gel, 10% MeOH–CH2Cl2) to give a pale-yellow solid; yield: 195 mg (45%); mp 145–146 °C (Lit.11 146–147 °C). IR (neat): 3163, 3031, 2954, 2931, 2871, 2803, 1715, 1691, 1664, 1477, 1365, 1170, 1034, 963, 862, 803, 761, 727, 636, 524 cm–1. 1H NMR (500 MHz, CDCl3): δ = 9.57 (s, 1 H, CH), 8.92 (br s, 1 H, NH), 6.24 (s, 1 H, CH), 4.19 (t, J = 7.8 Hz, 2 H, CH2), 1.61–1.55 (m, 2 H, CH2), 1.41–1.33 (m, 2 H, CH2), 0.95 (t J = 7.6 Hz, 3 H, CH3). 13C NMR (125 MHz, CDCl3): δ = 185.5, 164.4, 151.9, 146.9, 114.4, 43.7, 31.5, 19.7, 13.6. MALDI-TOF: m/z = 197.5 [M + H]+. 1-Hexyluracil-6-carbaldehyde (3b); Typical Procedures Method A: Compound 3b was prepared by the same procedure as 3a, starting from 2b (100 mg, 0.45 mmol) and SeO2 (50 mg, 0.45 mmol); yield: 43 mg (40%); pale-yellow solid; mp 149–150 °C. Method B: A suspension of 1-hexyluracil (8b; 200 mg, 1 mmol) in anhyd THF was stirred in a dry-ice bath (–78 °C) under argon. A 1 M solution of LDA in THF (10 mL) was added dropwise over 1 h, then HCO2Et (165 mL, 2 mmol) was slowly added from a syringe. The mixture was kept at –78 °C for 3 h then warmed to r.t. HOAc was added to neutralize excess base, and the mixture was filtered. The solvent was removed by rotary evaporation, and the crude product was purified by column chromatography (silica gel, 20% EtOAc–CH2Cl2) to give a yellow liquid; yield: 34 mg (15%). IR (KBr): 3129, 3073, 2965, 2925, 2858, 2781, 1709, 1659, 1645, 1601, 1474, 1396, 1371, 1182, 1057, 909, 836, 763, 720, 622, 544, 516 cm–1. 1H NMR (500 MHz, CDCl3): δ = 9.57 (s, 1 H, CH), 8.96 (s, 1 H, NH), 6.24 (s, 1 H, CH), 4.18 (t, J = 7.9 Hz, 2 H, CH2), 1.61–1.58 (m, 2 H, CH2), 1.35–1.31 (m, 6 H, CH2), 0.89 (t, J = 7.2 Hz, 3 H, CH3). 13C NMR (125 MHz, CDCl3): δ = 185.6, 162.4, 151.1, 146.9, 114.5, 43.9, 29.4, 26.1, 22.5, 19.9, 13.9. ESI-MS: m/z = 279.1 [M + CH3OH + Na]+.
  • 18 UracilBODIPY Derivatives 4; General Procedure The appropriate 1-substituted uracil-6-carbaldehyde 3 (1 equiv), DMP (2.1 equiv), and a catalytic amount of TFA were dissolved in anhyd CH2Cl2, and the mixture was stirred under argon at r.t. for 24 h. A solution of p-chloranil (1 equiv) in CH2Cl2 was added from a syringe, and the mixture was stirred for 1 h. Et3N (9 equiv) and BF3∙Et2O (6 equiv) were then added, and the mixture was stirred overnight. The organic fraction was washed with sat. aq NaHCO3 (50 ml), brine, and water, and the combined organic layers were dried (Na2SO4), filtered, and concentrated under reduced pressure. The resulting mixture was purified by column chromatography (silica gel, gradient 10–30% EtOAc–CH2Cl2). 1-ButyluracilBODIPY (4a) Prepared according to the general procedure from 3a (38 mg, 0.2 mmol) as a dark-red solid; yield: 28 mg (35%); mp 261–265 °C. IR (neat): 3156, 3035, 2960, 2926, 2874, 2798, 1714, 1670, 1541, 1509, 1457, 1410, 1309, 1187, 1152, 1053, 972, 798, 755, 607, 527, 475 cm–1. 1H NMR (500 MHz, CDCl3): δ = 9.66 (s, 1 H, NH), 6.12 (s, 2 H, CH), 5.84 (s, 1 H, CH), 3.70 (t, J = 8.2 Hz, 2 H, CH2), 2.57 (s, 6 H, CH3), 2.07 (s, 6 H, CH3), 1.52–1.48 (m, 2 H, CH2), 1.25–1.19 (m, 2 H, CH2), 0.76 (t, J = 7.5 Hz, 3 H, CH3). 13C NMR (125 MHz, CDCl3): δ = 162.2, 158.7, 151.1, 149.9, 141.7, 129.4, 127.8, 122.6, 103.7, 46.0, 30.2, 19.7, 14.9, 14.3, 13.2. MALDI-TOF: m/z = 415.4 [M + H]+.
    • 19a Kolemen S, Cakmak Y, Kostereli Z, Akkaya EU. Org. Lett. 2014; 16: 660
    • 19b Doulain P.-E, Goze C, Bodio E, Richard P, Decréau RA. Chem. Commun. 2016; 52: 4474
  • 20 Clarke R, Ho KL, Alsimaree AA, Woodford OJ, Waddell PG, Bogaerts J, Herrebout W, Knight JG, Pal R, Penfold TJ, Hall MJ. ChemPhotoChem 2017; 1: 513
  • 21 Castillo M, Raut SL, Price S, Bora I, Jameson LP, Qiu C, Schug KA, Gryczynski Z, Dzyuba SV. RSC Adv. 2016; 6: 68705
  • 22 Lakowicz JR. Principles of Fluorescence Spectroscopy, 2nd ed. Kluwer/Plenum; New York: 1999: 12