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Synlett 2015; 26(09): 1169-1174
DOI: 10.1055/s-0034-1380191
letter
© Georg Thieme Verlag Stuttgart · New York

Synthesis of a Toolbox of Clickable Rhodamine B Derivatives

Pierangelo Gobbo*
Department of Chemistry and the Centre for Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada   Email: mworkent@uwo.ca
,
Praveen Gunawardene
Department of Chemistry and the Centre for Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada   Email: mworkent@uwo.ca
,
Wilson Luo
Department of Chemistry and the Centre for Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada   Email: mworkent@uwo.ca
,
Mark S. Workentin*
Department of Chemistry and the Centre for Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada   Email: mworkent@uwo.ca
› Author Affiliations
Further Information

Publication History

Received: 27 January 2015

Accepted after revision: 23 February 2015

Publication Date:
18 March 2015 (online)

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Abstract

An efficient method for the large-scale preparation of rhodamine B clickable derivatives has been developed. Starting from inexpensive rhodamine B as the starting material it was possible to functionalize the carboxylic functionality of rhodamine B with an azide, a strained-alkyne, a substituted triphenylphosphine, a thiol, and a maleimide. Through the synthetic strategy it was possible to obtain stable and pure clickable rhodamine compounds that can be readily used not only for chemoselectively probing biomolecules, but also for materials science.

Key words

click chemistry - fluorescence spectroscopy - chromophore synthesis - Diels–Alder reaction - amide coupling

Supporting Information

    Supporting information for this article is available online at http://dx.doi.org/10.1055/s-0034-1380191.
  • Supporting Information
 

  • References and Notes

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    • 12a Synthesis of Rhodamine B–Piperazine 1 To a solution of rhodamine B (1.0 g, 2.1 mmol) and DIPEA (0.42 mL, 2.4 mmol) in MeCN (150 mL) and at 0 °C was added a solution of HBTU (0.91 g, 2.4 mmol) in MeCN (50 mL). After stirring the mixture for 30 min at 0 °C, an ice-cold solution of mono-Boc-piperazine (0.45 g, 2.4 mmol) in MeCN (20 mL) was added. The ice-bath was removed, and the reaction was left at r.t. for overnight. The solvent was removed by rotary evaporation, and the crude was directly purified by column chromatography on silica gel using CH2Cl2–EtOH 95% (15:1) as the eluent. To deprotect the piperazine moiety, the product was redissolved in 10% TFA (20 mL) in CH2Cl2, and the reaction mixture was stirred vigorously for 2 h at r.t. in an uncovered flask. The crude was concentrated by rotary evaporation, and TFA was removed by repeatedly redissolving the residue in acetone and reapplying the vacuum. The crude product was then purified by column chromatography using CH2Cl2–EtOH 95% (3:1) as the eluent and switching to CH2Cl2–EtOH 95% (3:2) as the eluent to collect pure rhodamine B–piperazine 1 as a shiny purple solid in 95% yield (1.25 g, 2.0 mmol). Rf  = 0.3 (CH2Cl2–95% EtOH, 3:1). 1H NMR (400 MHz, CDCl3): δ = 7.69–7.66 (m, 2 H), 7.59–7.57 (m, 1 H), 7.34–7.32 (m, 1 H), 7.16 (d, J = 12 Hz, 2 H), 6.92 (dd, J 1 = 12 Hz, J 2 = 4 Hz, 2 H), 6.73 (d, J = 4 Hz, 2 H), 3.75–3.51 (m, 12 H), 3.13 (br s, 2 H), 3.06 (br s, 2 H), 1.31 (t, J = 8 Hz, 12 H). 13C NMR (150 MHz, CDCl3): δ = 167.2, 157.7, 155.67, 155.51, 134.5, 130.84, 130.23, 130.20, 130.11, 127.7, 114.3, 113.6, 96.3, 90.5, 53.4, 46.0, 12.4. 19F NMR (376 MHz, CD3OD): δ = –76.89. ESI-HRMS: m/z calcd for C32H39N4O2 + [M]: 511.3068; found: 511.3074. IR (KBr): 3271,2983, 1683, 1647, 1590, 1528, 1468, 1415, 1339, 1276, 1248, 1203, 1179, 1131, 1075, 1010, 975, 922, 833, 799, 722, 682 cm–1. UV-vis (DMSO, λmax, ε): 571 nm, 91,573 M–1 cm–1.
    • 12b Synthesis of Rhodamine B–Azide 2 To a solution of 1 (0.243 g, 0.389 mmol) and DIPEA (140 μL, 0.804 mmol) in MeCN (3 mL) was added dropwise and at 0 °C a solution of 1-azido-3-iodopropane (2, 0.115 g, 0.545 mmol) in MeCN (1 mL). After stirring the mixture at r.t. overnight, the solvent was removed by rotary evaporation, and the resulting crude residue was purified by flash column chromatography (CH2Cl2–95% EtOH, 15:2) to yield 2 as a purple solid in 51% yield (0.140 g, 0.198 mmol). 1H NMR (400 MHz, CDCl3): δ = 7.71–7.69 (m, 2 H), 7.57–7.55 (m, 1 H), 7.38–7.36 (m, 1 H), 7.30 (d, J = 8 Hz, 2 H), 7.06 (d, J = 8 Hz, 2 H), 6.79 (d, J = 4 Hz, 2 H), 3.72–3.65 (m, 8 H), 3.42 (br s, 4 H), 3.35 (t, J = 8 Hz, 2 H), 2.38 (t, J = 8 Hz, 2 H), 2.35 (br s, 2 H), 2.28 (br s, 2 H), 1.74 (quin, J = 8 Hz, 2 H), 1.35 (t, J = 8 Hz, 12 H). 13C NMR (150 MHz, CD3OD): δ = 169.3, 159.3, 157.19, 157.00, 136.8, 133.35, 132.02, 131.61, 131.31, 131.11, 128.9, 115.5, 114.9, 97.4, 56.2, 54.1, 53.5, 50.5, 47.0, 42.7, 26.9, 12.9. 19F NMR (376 MHz, CDCl3): δ = –74.62. ESI-HRMS: m/z calcd for C35H44N7O2 + [M]: 594.3551; found: 594.3549. IR (KBr): 3262, 2924, 2029, 1630, 1588, 1413, 1339, 1273, 1179, 1131, 1073, 1007, 920,823, 680 cm–1. UV-vis (DMSO, λmax, ε): 571 nm, 91,102 M–1 cm–1.
    • 12c Synthesis of Rhodamine B–Trityl-Protected Thiol 5 To a solution of 1 (0.416g, 0.660 mmol) in acetone (2 mL) was added DIPEA (0.5 mL, 2.9 mmol). To this mixture was added a solution of (3-bromopropyl)(trityl)sulfane (4, 0.573 mg, 1.44 mmol) in acetone (12 mL). The mixture was stirred for 6 d at r.t. under Ar (g), after which the solvent was removed by rotary evaporation. The remaining crude residue was purified by flash column chromatography (CH2Cl2–95% EtOH, 7:2) to yield compound 5 as a shiny purple solid in 20% yield (120 mg, 0.128 mmol). 1H NMR (400 MHz, CD3OD): δ = 7.77–7.75 (m, 2 H), 7.64–7.63 (m, 1 H), 7.52–7.51 (m, 1 H), 7.37 (d, J = 8 Hz, 6 H), 7.28–7.18 (m, 11 H), 7.06 (dd, J 1 = 8 Hz, J 2 = 4 Hz, 2 H), 6.98 (d, J = 4 Hz, 2 H), 3.67 (q, J = 8 Hz, 8 H), 3.31 (br s, 4 H), 2.17–2.12 (m, 4 H), 2.03 (br s, 4 H), 1.41 (quin, J = 8 Hz, 2 H), 1.29 (t, J = 8 Hz, 12 H). 13C NMR (150 MHz, CD3OD): δ = 169.5, 159.4, 157.4, 156.7, 135.7, 133.5, 132.54, 132.04, 131.81, 131.59, 131.15, 130.6, 128.54, 127.6, 115.3, 114.7, 97.2, 67.7, 57.9, 53.8, 46.8, 42.5, 30.6, 26.4, 15.8, 12.8. ESI-HRMS: m/z calcd for C54H59N4O2S+ [M]: 827.4353; found: 827.4375.
    • 12d Synthesis of Rhodamine B–Furan-Protected Maleimide 8 To a solution of compound 1 (0.273 g, 0.437 mmol) in MeCN (1 mL) was added DIPEA (0.2 mL, 1.1 mmol). To this mixture was added a solution of compound 7 (0.242, 0.85mmol) MeCN (1 mL). The mixture was stirred for 3 d at r.t., after which the solvent was removed by rotary evaporation. The remaining crude residue was purified by flash column chromatography (CHCl3–95% EtOH, 3:2) to yield compound 8 as a shiny purple solid in 34% yield (105 mg, 0.127mmol). 1H NMR (400 MHz, CDCl3): δ = 7.66–7.63 (m, 2 H), 7.51–7.49 (m, 1 H), 7.33–7.31 (m, 1 H), 7.20 (d, J = 8 Hz, 2 H), 6.92 (dd, J 1 = 8 Hz, J 2 = 4 Hz, 2 H), 6.77 (d, J = 4 Hz, 2 H), 6.49 (s, 2 H), 5.19 (s, 2 H), 3.63 (q, J = 8 Hz, 8 H), 3.45 (t, J = 8 Hz, 2 H), 3.37 (br s, 2 H), 3.29 (br s, 2 H), 2.83 (s, 2 H), 2.29–2.16 (m, 6 H), 1.62 (quin, J = 8 Hz, 2 H), 1.31 (t, J = 8 Hz, 12 H). 13C NMR (150 MHz, CDCl3): δ = 176.0, 166.9, 157.5, 155.61, 155.34, 136.2, 135.2, 131.8, 130.3, 129.95, 129.78, 129.60, 127.3, 113.85, 113.45, 96.1, 80.7, 54.7, 52.69, 52.07, 47.28, 47.13, 45.90, 41.5, 36.6, 24.2, 12.4. ESI-HRMS: m/z calcd for C43H50N5O5 + [M]: 716.3806; found: 716.3817. IR (KBr): 3264, 2971, 1767, 1695, 1630, 1588, 1468, 1411, 1340, 1275, 1180, 1131, 1074, 1010, 920, 877, 822, 679 cm–1. UV-vis (DMSO, λmax, ε): 571 nm, 91,221 M–1 cm–1.
    • 12e Synthesis of Rhodamine B–Thiol 6 Compound 1 (0.135 g, 0.143 mmol) was dissolved in a solution of CH2Cl2–20% TFA (5 mL). To this solution was added i-Pr3SiH (60 μL, 0.29 mmol). The mixture was stirred for 2 d at r.t., after which the solvent was removed by rotary evaporation. The remaining crude residue was purified by flash column chromatography using CH2Cl2–95% EtOH (9:2) as the eluent to yield product 6 as a shiny purple solid in 50% yield (50 mg, 0.072 mmol). This compound must be handled and stored under inert atmosphere because it easily oxidizes to the corresponding disulphide. 1H NMR (400 MHz, CDCl3): δ = 7.66–7.59 (m, 2 H), 7.55–7.50 (m, 1 H), 7.32–7.25 (m, 1 H), 7.20 (d, J = 8 Hz, 2 H), 6.92 (dd, J 1 = 8 Hz, J 2 = 4 Hz, 2 H), 6.74 (d, J = 4 Hz, 2 H), 3.60 (q, J = 8 Hz, 8 H), 3.38 (br s, 2 H), 3.32 (br s, 2 H), 2.61 (t, J = 4 Hz, 2 H), 2.50–2.21 (m, 6 H), 1.82–1.62 (m, 3 H), 1.29 (t, J = 8 Hz, 12 H). 13C NMR (150 MHz, CDCl3): δ = 169.5, 159.4, 157.4, 156.7, 135.7, 133.5, 132.54, 132.04, 131.81, 131.59, 128.94, 128.14, 115.5, 114.9, 97.5, 56.9, 53.8, 47.68, 47.02, 39.5, 29.0, 22.0, 13.0. 19F NMR (376 MHz, CDCl3): δ = –74.62. ESI-HRMS: m/z calcd for C35H45N4O2S+ [M]: 585.3258; found: 585.3263. IR (KBr): 3362, 3064, 2969, 2927, 2806, 1689, 1635, 1589, 1469, 1415, 1340, 1275, 1250, 1180, 1228, 1074, 1008, 972, 921, 822, 792, 721, 680 cm–1. UV-vis (DMSO, λmax, ε): 571 nm, 89,842 M–1 cm–1.
    • 12f Synthesis of Rhodamine B–Maleimide 9 Compound 8 (0.050g, 0.080 mmol) was dissolved in DMF (0.5 mL) and heated to 110 °C for 5 h. The DMF was removed by rotary evaporation by dilution with toluene. The resulting residue was purified by flash column chromatography (CH2Cl2–95% EtOH, 7:1) to yield product 9 as a shiny purple solid in 66% yield (0.040 g, 0.053 mmol). 1H NMR (400 MHz, CDCl3): δ = 7.67–7.65 (m, 2 H), 7.51–7.49 (m, 1 H), 7.34–7.32 (m, 1 H), 7.22 (d, J = 8 Hz, 2 H), 6.95 (dd, J 1 = 8 Hz, J 2 = 4 Hz, 2 H), 6.79 (d, J = 4 Hz, 2 H), 6.67 (s, 2 H), 3.64 (q, J = 8 Hz, 8 H), 3.52 (t, J = 8 Hz, 2 H), 3.39 (br s, 2 H), 3.33 (br s, 2 H), 2.33–2.20 (m, 6 H), 1.70 (quin, J = 8 Hz, 2 H), 1.31 (t, J = 8 Hz, 12 H). 13C NMR (150 MHz, CD3OD): δ = 172.6, 159.4, 157.03, 157.07, 135.6, 133.5, 131.71, 131.43, 131.20, 129.0, 115.54, 115.00, 97.5, 95.81, 56.8, 54.2, 53.7, 47.1, 42.9, 40.6, 30.8, 26.3, 13.02. 19F NMR (376 MHz, CD3OD): δ = –50.00. ESI-HRMS): m/z calcd for C39H46N5O4 + [M]: 648.3544; found: 648.3543. IR (KBr): 3256, 2973, 2930, 2872, 1705, 1631, 1590, 1556, 1528, 1508, 1469, 1414, 1341, 1276, 1249, 1181, 1133, 1075, 1011, 976, 922, 827, 761, 683 cm–1. UV-vis (DMSO, λmax, ε): 571 nm, 90,419 M–1 cm–1.
    • 12g Synthesis of Rhodamine B–BCN 11 To a solution of 1 (0.27 g, 0.43 mmol) and DIPEA (150 μL, 0.861 mmol) in MeCN was added dropwise and at 0 °C a solution of compound 10 (0.080 g, 0.25 mmol) in MeCN (1 mL). After the reaction mixture was stirred at r.t. for 20 h, the solvent was removed by rotary evaporation, and the resulting crude residue was purified by flash column chromatography (CH2Cl2–i-PrOH, 7:3) to yield product 11 as a shiny purple solid in 88% yield (175 mg, 0.219 mmol). 1H NMR (400 MHz, CD3OD): δ = 7.78–7.76 (m, 2 H), 7.70–7.68 (m, 1 H), 7.53–7.50 (m, 1 H), 7.28 (d, J = 8 Hz, 2 H), 7.07 (dd, J 1 = 8 Hz, J 2 = 4 Hz, 2 H), 7.67 (d, J = 4 Hz, 2 H), 3.98 (d, J = 8 Hz, 2 H), 3.69 (q, J = 8 Hz, 8 H), 3.39 (br s, 4 H), 3.31 (br s, 4 H), 2.37–2.29 (m, 2 H), 2.29–2.06 (m, 4 H), 1.42–1.29 (m, 14 H), 0.75–0.64 (m, 3 H). 13C NMR (150 MHz, CD3CN): δ = 168.5, 162.52, 162.27, 159.0, 157.2, 156.93, 156.54, 136.8, 133.2, 132.04, 131.39, 131.11, 130.9, 128.8, 116.7, 115.3, 114.8, 99.8, 97.2, 71.0, 46.9, 34.3, 31.1, 24.7, 23.9, 22.0, 14.4, 13.0. 19F NMR (376 MHz, CD3CN): δ = –76.26. ESI-HRMS: m/z calcd for C43H51N4O4 + [M]: 687.391; found: 687.393. IR (KBr): 3255, 2977,2923, 1675,1589, 1419, 1340, 1254, 1183, 1132, 1077, 1006, 922, 831, 721, 679 cm–1. UV-vis (DMSO, λmax, ε): 571 nm, 91,299 M–1 cm–1.
    • 12h Synthesis of Rhodamine B–Triphenylphosphine 13 To a flask containing compound 1 (50 mg, 0.080 mmol), HBTU (520 mg, 0.137 mmol), and 3-(diphenylphosphino)-4-(methoxycarbonyl)benzoic acid (12, 390 mg, 0.108 mmol) were added MeCN (2 mL) and DIPEA (0.040 mL, 0.23 mmol). The reaction mixture was stirred for 18 h. The solvent was removed under reduced pressure, and the crude product was purified by flash chromatography using i-PrOH–CH2Cl2 (1:10) as the eluent to give the product 13 as a purple solid in 51% yield (40 mg, 0.041 mmol). 1H NMR (400 MHz, CDCl3): δ = 8.08 (br s, 1 H), 7.72–7.62 (m, 3 H), 7.56–7.39 (m, 4 H), 7.37–7.18 (m, 11 H), 6.94–6.70 (m, 4 H), 3.71 (s, 3 H), 3.64–3.51 (m, 10 H), 3.37 (br s, 4 H), 3.22 (br s, 2 H), 1.29 (t, J = 8 Hz, 12 H). 13C NMR (150 MHz, CDCl3): δ = 169.3, 167.6, 166.5, 157.7, 155.6, 141.1, 140.8, 137.63, 137.31, 134.6, 134.0, 133.8, 132.4, 131.9, 131.3, 130.44, 130.30, 128.81, 128.66, 128.58, 128.41, 127.75, 127.48, 114.1, 113.7, 96.3, 64.3, 52.2, 46.0, 41.7, 30.9, 25.3,12.5. 31P NMR (162 MHz, CDCl3): δ = –3.80 (s). ESI-HRMS: m/z calcd for C53H54N4O5P+ [M]: 857.3826; found: 857.3822. IR (KBr): 3254, 3054, 2973, 2929, 2869, 1718, 1635, 1589, 1527, 1466, 1414, 1338, 1274, 1247, 1180, 1159, 1132, 1073, 1004, 975, 921, 840, 789, 748, 698, 682, 664 cm–1. UV-vis (DMSO, λmax, ε): 571 nm, 88,970 M–1 cm–1.
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