Reactions of BODIPY Fluorophore with Cupric Nitrate

Abstract

4,4-Difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) and corresponding 4,4-dimethyl and 4,4-diphenyl analogues were treated with cupric nitrate trihydrate under different conditions. Corresponding 3-nitro-, nitromethyl-, hydroxymethyl BODIPY, and BODIPY 3-carboxyaldehyde were obtained. The UV/vis and fluorescent properties of these BODIPY analogues were determined.

4,4-Difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) fluorophores have gained increasing popularity in recent years due to their unique fluorescent properties.[2] A number of these fluorophores have been used to label biomolecules such as peptides, proteins, lipids, and nucleic acids. These BODIPY fluorophores have also found increasingly broad applications in sensors and molecular devices.[2]

Despite the numerous new reactions that were discovered for the functionalization of BODIPY fluorophores, introduction of functional groups to BODIPY that allow for further transformations remains relatively challenging. Three recent reports demonstrated attractive synthetic approaches towards the functionalization of BODIPY fluorophores.[3] Of particular interest was the work reported by Bañuelos and coworkers,[3b] where the nitro group was introduced into BODIPY fluorophore either from nitropyrrole or by the nitration of BODIPY with nitric acid in the presence of acetic anhydride. A similar approach was reported towards the direct nitration of BODIPY, which gave 2- or 2,6-dinitro BODIPY (instead of 3-nitro BODIPY).[3c] Whereas nitropyrrole derivatives are difficult to synthesize, nitration of BODIPY by nitric acid in the presence of acetic anhydride lacks selectivity, which invariably led to the formation of regioisomers. As a related series of compounds, amino BODIPY analogues are useful precursors for further transformation; however, access to amino BODIPY has also been rather limited.[4]

We wish to disclose herein an approach for the access of BODIPY analogues bearing functional groups of high synthetic utility such as nitro, aldehyde, and hydroxyl groups (Scheme [1]). This approach entails treatment of BODIPY with cupric nitrate trihydrate or a mixture of ­nitrates in acetonitrile to give BODIPY analogues in moderate yields. Thus, when 4,4-difluoro-1,3,5,7,8-penta­methyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (1) was treated with half molar equivalent of cupric nitrate trihydrate in wet acetonitrile and dichloromethane (containing 0.004% water), 4,4-difluoro-3-nitromethyl-1,5,7,8-tetramethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (2) was isolated in 54% yield after column chromatography.[5] Interestingly, treatment of 4,4-difluoro-1,3,5,7,8-penta­methyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (1) with five molar equivalents of cupric nitrate trihydrate in dry acetonitrile and dichloromethane led to the formation of a mixture of 4,4-difluoro-3-nitro-1,5,7,8-tetramethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (3) and 4,4-difluoro-1,5,7,8-tetramethyl-2,6-diethyl-4-bora-3a,4a-di­aza-s-indacene-3-carboxyaldehyde (4) in an approximately 6:1 ratio as determined by NMR spectroscopy.[6]

The structures of BODIPY analogues 2 and 3 were confirmed by X-ray crystallography (Figure [1]). It is noted that 3-nitromethyl BODIPY (2) has a pseudo twofold rotation axis through the middle of the molecule, whereas the oxygen atoms of the nitro group in 3-nitro BODIPY (3) are disordered and there are some weak C–H···O and C–H···F interactions (Figure [2]).

It was further observed that treatment of 4,4-difluoro-1,3,5,7,8-pentamethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (1) with ten molar equivalents of calcium nitrate in the presence of 0.1 molar equivalent of cupric nitrate trihydrate in a mixture of acetonitrile and dichloromethane containing 0.02% water led to the formation of 4,4-difluoro-3-hydroxymethyl-1,5,7,8-tetramethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (5) in 50% isolated yield.

It is of interest to note that this transformation is not unique for 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (1). Thus, it was found that treatment of 4,4-dimethyl- (6a)[8] and 4,4-diphenyl- (6b)[8b] [9] BODIPY analogues with five molar equivalents of cupric nitrate trihydrate in dry acetonitrile and dichloromethane also led to the formation of the corresponding 3-nitro-BODIPY 7a and 7b, respectively (Scheme [2]).

The transformations described above for the formation of 3-nitro-substituted BODIPY (3) appear to only occur when reactions were carried out under dry conditions; whereas the other transformations underwent smoothly in acetonitrile and dichloromethane that were prepared by adding a specific amount of water to the corresponding dry solvents.

The UV/vis and fluorescent properties of the functionalized BODIPY analogues were characterized (Table [1]). As anticipated, the fluorescence of 3-nitro BODIPY analogues 3 and 7a,b is virtually quenched due to the electron-withdrawing properties of nitro group.

The mechanism for the reaction of BODIPY with cupric nitrate is unclear at this time, however, it was observed that when cupric nitrate is replaced with sodium nitrate, calcium nitrate, silver nitrate, cupric acetate, cupric chloride, or cupric sulfate alone, BODIPY did not undergo the reactions described in Scheme [1]. The reaction (1 → 3, Scheme [1]) does not seem to involve radicals, as addition of excess of triethylsilane or 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) to BODIPY (1) followed by addition of cupric nitrate did not affect the outcome of the reactions. Further, in dry acetonitrile, this reaction (1 → 3, Scheme [1]) appears to be oxygen-dependent. Thus, in the absence of oxygen, 3-nitromethyl BODIPY (2, instead of 3-nitro BODIPY 3) was formed as the major product. It was originally speculated that 3-nitromethyl BODIPY 2 might be the intermediate towards the formation of 3-nitro BODIPY 3; however, treatment of 3-nitromethyl BODIPY (2) with five molar equivalents of cupric nitrate in dry acetonitrile did not lead to the formation of 3-nitro BODIPY 3. In this latter case, corresponding BODIPY aldehyde 4 was found to be the main product. It is noted that in the absence of cupric nitrate, BODIPY aldehyde 4 was not formed when nitromethyl BODIPY 2 was kept in dichloromethane–acetonitrile overnight.

In an effort to rationalize the role of solvent in the transformation (1 → 3), BODIPY (1) was treated with cupric nitrate trihydrate (10 mol equiv) in dry DMF, THF, DMSO, and acetone, respectively. No reaction was observed under these conditions. These observations seem to suggest that hydrated water plays a role in this transformation. Considering the observation that the donor strengths of DMF, THF, DMSO, and acetone are greater than those of dichloromethane and acetonitrile,[11] it is conceivable that hydrate water is displaced in solvents such as DMF, THF, DMSO, and acetone; however, the full extent of this hypothesis is not understood at this time.

Some of the BODIPY analogues described herein can be useful intermediates for further transformation or they can be used towards the preparation of fluorescent labeling agents. One compound, 3-nitro BODIPY 3, is of particular interest. As noted in Table [1], the fluorescence of 3 is virtually quenched (Φ = 0.01), however, upon reduction by catalytic hydrogenation (Scheme [3]), the corresponding 3-amino BODIPY 8 is rather fluorescent (Φ = 0.40). It is anticipated that this compound could be useful as a fluorescent turn-on sensor for reductive environments.

To summarize, 3-nitro-, nitromethyl, hydroxylmethyl BODIPY, and BODIPY 3-carboxyldehyde were prepared by the treatment with cupric nitrate trihydrate under different conditions. These compounds are useful intermediates for further transformation of BODIPY. Applications of these BODIPY analogues in this respect are currently under investigation in this laboratory.

Acknowledgment

The authors wish to thank the Natural Science and Engineering Research Council of Canada for funding this work.

• References and Notes

• 1 These authors contributed equally to this work.
• 2a Ulrich G, Ziessel R, Harriman A. Angew. Chem. Int. Ed. 2008; 47: 1184
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• 2b Loudet A, Burgess K. Chem. Rev. 2007; 107: 4891
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• 2c Ziessel R, Ulrich G, Harriman A. New J. Chem. 2007; 496
• 3a Ulrich G, Ziessel R, Haefele A. J. Org. Chem. 2012; 77: 4298
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• 3b Esnal I, Banuelos J, Arbeloa IL, Costela A, Garcia-Moreno I, Garzon M, Agarrabeitia AR, Ortiz MJ. RSC Adv. 2013; 3: 1547
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• 3c Gupta M, Mula S, Tyagi M, Ghanty TK, Murudkar S, Ray AK, Chattopadhyay S. Chem. Eur. J. 2013; 19: 17766
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• 4a Ganapathi E, Madhu S, Chatterjee T, Gonnade R, Ravikanth M. Dyes Pigments 2014; 102: 218
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• 4b Liras M, Prieto JB, Pintado-Sierra M, Arbeloa FL, Garcia-Moreno I, Costela Á, Infantes L, Sastre R, Amat-Guerri F. Org. Lett. 2007; 9: 4183
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• 5 Procedure for the Synthesis of 4,4-Difluoro-3-nitromethyl-1,5,7,8-tetramethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (2) To a solution of 4,4-difluoro-1,3,5,7,8-pentamethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (1, 100 mg, 0.31 mmol) in CH₂Cl₂ [20 mL, CH₂Cl₂ was first dried by heating in the presence of P₄O₁₀ and distilled, and then 0.004% H₂O (v/v) was added], a solution of Cu(NO₃)₂·3H₂O in MeCN [0.41 M, 0.38 mL, 0.5 mol equiv, MeCN was first dried by heating in the presence of CaH₂ and distilled, and then 0.004% H₂O (v/v) was added] was added. After the mixture was stirred for 3 h, the products were evaporated under reduced pressure. The residue was redissolved in CH₂Cl₂ (20 mL) and extracted with H₂O (3 × 15 mL). The organic layer was separated, dried (MgSO₄) and evaporated under reduced pressure. The residue was purified by column chromatog-raphy on silica gel. The appropriate fractions, which were eluted with CH₂Cl₂–hexane (50:50, v/v), were combined and evaporated under reduced pressure to give the title compound as a red solid (61 mg, 54%); mp 196–200 °C (CH₂Cl₂–hexanes). R_f = 0.87 (CH₂Cl₂). ¹H NMR (300.1 MHz, CDCl₃): δ = 1.07 (3 H, t, J = 7.6 Hz), 1.10 (3 H, t, J = 7.6 Hz), 2.39 (3 H, s), 2.40 (3 H, s), 2.43 (2 H, q, J = 7.6 Hz), 2.48 (2 H, q, J = 7.6 Hz), 2.55 (3 H, s), 2.70 (3 H, s), 5.72 (2 H, s). ¹³C NMR (75.5 MHz, CDCl₃): δ = 13.0, 14.1, 14.5,14.7, 14.9, 17.1, 17.2, 17.3, 69.4, 131.8, 133.6, 133.9, 134.6, 135.6, 140.9, 142.2, 159.9. ¹¹B NMR (96.3 MHz, CDCl₃): δ = 0.47 (t, J = 33.3 Hz). ¹⁹F NMR (282.4 MHz, CDCl₃): δ = –143.6 (q, J = 33.3). HRMS (EI): m/z calcd for C₁₈H₂₄BF₂N₃O₂: 363.19296; found: 363.19288.
• 6 Procedure for the Synthesis of 4,4-Difluoro-3-nitro-1,5,7,8-tetramethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (3) To a solution of 4,4-methyl-1,3,5,7,8-pentamethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (1, 100 mg, 0.31 mmol) in dry CH₂Cl₂ (20 mL), a solution of Cu(NO₃)₂·3H₂O (380 mg, 5 mol equiv) in dry MeCN (10 mL) was added. After the mixture was stirred for 5 min, the products were evaporated under reduced pressure. The residue was redissolved in CH₂Cl₂ (30 mL) and extracted with H₂O (3 × 20 mL). The organic layer was separated, dried (MgSO₄), and evaporated under reduced pressure. The residue was purified by column chromatography on silica gel. The appropriate fractions, which were eluted with CH₂Cl₂–hexane (70:30, v/v), were combined and evaporated under reduced pressure to give the title compound as a red solid (42 mg, 38%); mp 212–216 °C (CH₂Cl₂–hexanes). R_f = 0.42 (system A). ¹H NMR (300.1 MHz, CDCl₃): δ = 1.09 (3 H, t, J = 7.5 Hz), 1.16 (3 H, t, J = 7.5 Hz), 2.37 (3 H, s), 2.41 (3 H, s), 2.46 (2 H, q, J = 7.5 Hz), 2.64 (3 H, s), 2.72 (2 H, q, J = 7.5 Hz), 2.73 (3 H, s). ¹³C NMR (75.5 MHz, CDCl₃): δ = 13.4, 13.7, 14.1, 14.2, 14.9, 17.1, 17.9, 18.3, 130.0, 130.2, 130.4, 137.6, 138.8, 141.5, 142.7, 144.3, 166.8. ¹⁹F NMR (282.4 MHz, CDCl₃): δ = –144.6 (q, J = 29.2 Hz). ¹¹B NMR (96.3 MHz, CDCl₃): δ = 0.30 (t, J = 28.2 Hz). HRMS (EI): m/z calcd for C₁₇H₂₂BF₂N₃O₂: 349.17731; found: 349.17713. It is noted that this reaction gave a mixture of 4,4-difluoro-3-nitro-1,5,7,8-tetramethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (3) and 4,4-difluoro-1,5,7,8-tetramethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene-3-carboxyaldehyde (4, with a total mass of 78 mg) in a ratio of 6.3:1 as determined by ¹H NMR spectroscopy. Therefore, the overall yield of the title compound is 62%. In addition to the pure 4,4-difluoro-3-nitro-1,5,7,8-tetramethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (3, 42 mg), separation of the rest of product 3 from contaminating aldehyde 4 was rather difficult.
• 7 Spek AL. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2009; 65: 148
  CrossrefSearch in Google Scholar
• 8a Li L, Nguyen B, Burgess K. Bioorg. Med. Chem. Lett. 2008; 18: 3112
  CrossrefSearch in Google Scholar
• 8b Yang L, Simionescu R, Lough A, Yan H. Dyes Pigments 2011; 91: 264
  CrossrefSearch in Google Scholar
• 9 Goze C, Ulrich G, Mallon LJ, Allen BD, Harriman A, Ziessel R. J. Am. Chem. Soc. 2006; 128: 10231
  CrossrefSearch in Google Scholar
• 10 Lacowicz JR. Principles of Fluorescence Spectroscopy . Springer; New York: 2006. 3rd ed.; Chap. 2, 54
  CrossrefSearch in Google Scholar
• 11 Sandström M, Persson I, Persson P. Acta Chim. Scand. 1990; 44: 653
  CrossrefSearch in Google Scholar

• References and Notes

• 1 These authors contributed equally to this work.
• 2a Ulrich G, Ziessel R, Harriman A. Angew. Chem. Int. Ed. 2008; 47: 1184
  CrossrefPubMedSearch in Google Scholar
• 2b Loudet A, Burgess K. Chem. Rev. 2007; 107: 4891
  CrossrefPubMedSearch in Google Scholar
• 2c Ziessel R, Ulrich G, Harriman A. New J. Chem. 2007; 496
• 3a Ulrich G, Ziessel R, Haefele A. J. Org. Chem. 2012; 77: 4298
  CrossrefSearch in Google Scholar
• 3b Esnal I, Banuelos J, Arbeloa IL, Costela A, Garcia-Moreno I, Garzon M, Agarrabeitia AR, Ortiz MJ. RSC Adv. 2013; 3: 1547
  CrossrefSearch in Google Scholar
• 3c Gupta M, Mula S, Tyagi M, Ghanty TK, Murudkar S, Ray AK, Chattopadhyay S. Chem. Eur. J. 2013; 19: 17766
  CrossrefSearch in Google Scholar
• 4a Ganapathi E, Madhu S, Chatterjee T, Gonnade R, Ravikanth M. Dyes Pigments 2014; 102: 218
  CrossrefSearch in Google Scholar
• 4b Liras M, Prieto JB, Pintado-Sierra M, Arbeloa FL, Garcia-Moreno I, Costela Á, Infantes L, Sastre R, Amat-Guerri F. Org. Lett. 2007; 9: 4183
  CrossrefSearch in Google Scholar
• 5 Procedure for the Synthesis of 4,4-Difluoro-3-nitromethyl-1,5,7,8-tetramethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (2) To a solution of 4,4-difluoro-1,3,5,7,8-pentamethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (1, 100 mg, 0.31 mmol) in CH₂Cl₂ [20 mL, CH₂Cl₂ was first dried by heating in the presence of P₄O₁₀ and distilled, and then 0.004% H₂O (v/v) was added], a solution of Cu(NO₃)₂·3H₂O in MeCN [0.41 M, 0.38 mL, 0.5 mol equiv, MeCN was first dried by heating in the presence of CaH₂ and distilled, and then 0.004% H₂O (v/v) was added] was added. After the mixture was stirred for 3 h, the products were evaporated under reduced pressure. The residue was redissolved in CH₂Cl₂ (20 mL) and extracted with H₂O (3 × 15 mL). The organic layer was separated, dried (MgSO₄) and evaporated under reduced pressure. The residue was purified by column chromatog-raphy on silica gel. The appropriate fractions, which were eluted with CH₂Cl₂–hexane (50:50, v/v), were combined and evaporated under reduced pressure to give the title compound as a red solid (61 mg, 54%); mp 196–200 °C (CH₂Cl₂–hexanes). R_f = 0.87 (CH₂Cl₂). ¹H NMR (300.1 MHz, CDCl₃): δ = 1.07 (3 H, t, J = 7.6 Hz), 1.10 (3 H, t, J = 7.6 Hz), 2.39 (3 H, s), 2.40 (3 H, s), 2.43 (2 H, q, J = 7.6 Hz), 2.48 (2 H, q, J = 7.6 Hz), 2.55 (3 H, s), 2.70 (3 H, s), 5.72 (2 H, s). ¹³C NMR (75.5 MHz, CDCl₃): δ = 13.0, 14.1, 14.5,14.7, 14.9, 17.1, 17.2, 17.3, 69.4, 131.8, 133.6, 133.9, 134.6, 135.6, 140.9, 142.2, 159.9. ¹¹B NMR (96.3 MHz, CDCl₃): δ = 0.47 (t, J = 33.3 Hz). ¹⁹F NMR (282.4 MHz, CDCl₃): δ = –143.6 (q, J = 33.3). HRMS (EI): m/z calcd for C₁₈H₂₄BF₂N₃O₂: 363.19296; found: 363.19288.
• 6 Procedure for the Synthesis of 4,4-Difluoro-3-nitro-1,5,7,8-tetramethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (3) To a solution of 4,4-methyl-1,3,5,7,8-pentamethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (1, 100 mg, 0.31 mmol) in dry CH₂Cl₂ (20 mL), a solution of Cu(NO₃)₂·3H₂O (380 mg, 5 mol equiv) in dry MeCN (10 mL) was added. After the mixture was stirred for 5 min, the products were evaporated under reduced pressure. The residue was redissolved in CH₂Cl₂ (30 mL) and extracted with H₂O (3 × 20 mL). The organic layer was separated, dried (MgSO₄), and evaporated under reduced pressure. The residue was purified by column chromatography on silica gel. The appropriate fractions, which were eluted with CH₂Cl₂–hexane (70:30, v/v), were combined and evaporated under reduced pressure to give the title compound as a red solid (42 mg, 38%); mp 212–216 °C (CH₂Cl₂–hexanes). R_f = 0.42 (system A). ¹H NMR (300.1 MHz, CDCl₃): δ = 1.09 (3 H, t, J = 7.5 Hz), 1.16 (3 H, t, J = 7.5 Hz), 2.37 (3 H, s), 2.41 (3 H, s), 2.46 (2 H, q, J = 7.5 Hz), 2.64 (3 H, s), 2.72 (2 H, q, J = 7.5 Hz), 2.73 (3 H, s). ¹³C NMR (75.5 MHz, CDCl₃): δ = 13.4, 13.7, 14.1, 14.2, 14.9, 17.1, 17.9, 18.3, 130.0, 130.2, 130.4, 137.6, 138.8, 141.5, 142.7, 144.3, 166.8. ¹⁹F NMR (282.4 MHz, CDCl₃): δ = –144.6 (q, J = 29.2 Hz). ¹¹B NMR (96.3 MHz, CDCl₃): δ = 0.30 (t, J = 28.2 Hz). HRMS (EI): m/z calcd for C₁₇H₂₂BF₂N₃O₂: 349.17731; found: 349.17713. It is noted that this reaction gave a mixture of 4,4-difluoro-3-nitro-1,5,7,8-tetramethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (3) and 4,4-difluoro-1,5,7,8-tetramethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene-3-carboxyaldehyde (4, with a total mass of 78 mg) in a ratio of 6.3:1 as determined by ¹H NMR spectroscopy. Therefore, the overall yield of the title compound is 62%. In addition to the pure 4,4-difluoro-3-nitro-1,5,7,8-tetramethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (3, 42 mg), separation of the rest of product 3 from contaminating aldehyde 4 was rather difficult.
• 7 Spek AL. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2009; 65: 148
  CrossrefSearch in Google Scholar
• 8a Li L, Nguyen B, Burgess K. Bioorg. Med. Chem. Lett. 2008; 18: 3112
  CrossrefSearch in Google Scholar
• 8b Yang L, Simionescu R, Lough A, Yan H. Dyes Pigments 2011; 91: 264
  CrossrefSearch in Google Scholar
• 9 Goze C, Ulrich G, Mallon LJ, Allen BD, Harriman A, Ziessel R. J. Am. Chem. Soc. 2006; 128: 10231
  CrossrefSearch in Google Scholar
• 10 Lacowicz JR. Principles of Fluorescence Spectroscopy . Springer; New York: 2006. 3rd ed.; Chap. 2, 54
  CrossrefSearch in Google Scholar
• 11 Sandström M, Persson I, Persson P. Acta Chim. Scand. 1990; 44: 653
  CrossrefSearch in Google Scholar

• Supplementary Material