BODIPY

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BODIPY
BODIPY.svg
Names
Preferred IUPAC name
5,5-Difluoro-5H-4λ5-dipyrrolo[1,2-c:2′,1′-f][1,3,2]diazaborinin-4-ylium-5-uide
Other names
Dipyrrometheneboron difluoride
Identifiers
3D model (JSmol)
8139995
ChEBI
ChEMBL
ChemSpider
PubChem CID
  • InChI=1S/C9H7BF2N2/c11-10(12)13-5-1-3-8(13)7-9-4-2-6-14(9)10/h1-7H
    Key: GUHHEAYOTAJBPT-UHFFFAOYSA-N
  • [B-]1(N2C=CC=C2C=C3[N+]1=CC=C3)(F)F
Properties
C9H7BF2N2
Molar mass 191.98 g/mol
Appearancered crystalline solid [1]
Melting point 450 °C [1]
Solubility methanol, dichloromethane [1]
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
Samples of halogenated BODIPY dyes in ambient lighting and fluorescing under UV Series of halogenated BODIPY molecules in ambient lighting and fluorescing under UV.png
Samples of halogenated BODIPY dyes in ambient lighting and fluorescing under UV

BODIPY is the technical common name of a chemical compound with formula C
9H
7BN
2F
2, whose molecule consists of a boron difluoride group BF
2 joined to a dipyrromethene group C
9H
7N
2; specifically, the compound 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene in the IUPAC nomenclature. [1] The common name is an abbreviation for "boron-dipyrromethene". It is a red crystalline solid, stable at ambient temperature, soluble in methanol. [1]

Contents

The compound itself was isolated only in 2009, [2] [1] [3] but many derivatives—formally obtained by replacing one or more hydrogen atoms by other functional groups—have been known since 1968, and comprise the important class of BODIPY dyes. [4] These organoboron compounds have attracted much interest as fluorescent dyes and markers in biological research. [1]

Structure

In its crystalline solid form, the core BODIPY is almost, but not entirely, planar and symmetrical; except for the two fluorine atoms, that lie on the perpendicular bisecting plane. [1] Its bonding can be explained by assuming a formal negative charge on the boron atom, and a formal positive charge on one of the nitrogen atoms.

Synthesis

BODIPY and its derivatives can be obtained by reacting the corresponding 2,2'-dipyrromethene derivatives with boron trifluoride-diethyl ether complex (BF
3·(C
2H
5)
2O) in the presence of triethylamine or 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU). [1] The difficulty of the synthesis was due to instability of the usual dipyrromethene precursor, rather than of BODIPY itself. [1] [5]

The dipyrromethene precursors are accessed from a suitable pyrrole derivatives by several methods. Normally, one alpha-position in employed pyrroles is substituted and the other is free. Condensation of such pyrrole, often available from Knorr pyrrole synthesis, with an aromatic aldehyde in the presence of trifluoroacetic acid gives dipyrromethane, which is oxidized to dipyrromethene using a quinone oxidant such as DDQ [1] or p-chloranil. [6]

Alternatively, dipyrromethenes are prepared by treating a pyrrole with an activated carboxylic acid derivative, usually an acyl chloride. Unsymmetrical dipyrromethenes can be obtained by condensing pyrroles with 2-acylpyrroles. Intermediate dipyrromethanes may be isolated and purified, but isolation of dipyrromethenes is usually compromised by their instability.

BODIPY synth.png

Derivatives

IUPAC atom numbering for substitutions on the BODIPY core. Positions 3 and 5 are also commonly called "a"; 1,2,6,7 are called "b"; and 8 is called "meso". Note that the numbering does not match the numbering on the parent 2,2'-dipyrromethene molecule. BODIPY core numbering.png
IUPAC atom numbering for substitutions on the BODIPY core. Positions 3 and 5 are also commonly called "α"; 1,2,6,7 are called "β"; and 8 is called "meso". Note that the numbering does not match the numbering on the parent 2,2'-dipyrromethene molecule.
Molecular structure of 1,3,5,7-tetramethyl-8-phenyl-substituted BODIPY. COCHEJ01.png
Molecular structure of 1,3,5,7-tetramethyl-8-phenyl-substituted BODIPY.

The BODIPY core has a rich derivative chemistry due to the high tolerance for substitutions in the pyrrole and aldehyde (or acyl chloride) starting materials. [5]

Hydrogen atoms at the 2 and 6 positions of the cyclic core can be displaced by halogen atoms using succinimide reagents such as NCS, NBS and NIS - which allows for further post-functionalisation through palladium coupling reactions with boronate esters, tin reagents etc. [5]

The two fluorine atoms on the boron atom can be replaced, during or after synthesis, by other strong nucleophilic reagents, such as lithiated alkyne or aryl species, [5] chlorine, [6] methoxy, [6] or a divalent "strap". [9] The reaction is catalysed by BBr3 or SnCl4. [10]

Fluorescence

BODIPY and many of its derivatives have received attention recently for being fluorescent dyes with unique properties. They strongly absorb UV-radiation and re-emit it in very narrow frequency spreads, with high quantum yields, mostly at wavelengths below 600 nm. They are relatively insensitive to the polarity and pH of their environment and are reasonably stable to physiological conditions. Small modifications to their structures enable tuning of their fluorescence characteristics. [7] BODIPY dyes are relatively chemically inert. Fluorescence is quenched in a solution, which limits application. This problem has been handled by synthesizing asymmetric boron complexes and replacing the fluorine groups with phenyl groups.

The unsubstituted BODIPY has a broad absorption band, from about 420 to 520 nm (peaking at 503 nm) and a broad emission band from about 480 to 580 nm (peaking at 512 nm), with a fluorescence lifetime of 7.2 ns. Its fluorescence quantum yield is near 1, greater than that of substituted BODIPY dyes and comparable to those of rhodamine and fluorescein, but fluorescence is lost above 50 °C. [2]

BODIPY dyes are notable for their uniquely small Stokes shift, high, environment-independent fluorescence quantum yields, often approaching 100% even in water, sharp excitation and emission peaks contributing to overall brightness, and high solubility in many organic solvents. The combination of these qualities makes BODIPY fluorophores promising for imaging applications. The position of the absorption and emission bands remain almost unchanged in solvents of different polarity as the dipole moment and transition dipole are mutually orthogonal.

Potential applications

The advantages of BODIPY are their low photodegradation, low toxicity and polarity, high biocompatibility, charge neutrality, and high fluorescence quantum yield, all of which make BODIPY effective markers. [11] [12] BODIPY conjugates are widely studied as potential sensors and for labelling biobjects (e.g. cell organelles) [13] [14] [15] [16] by exploiting its highly tunable optoelectronic properties. [17] [18] [19] [20] [21] [22] [23]

Numerous BODIPY derivatives are being investigated as electroactive species for single-substance redox flow batteries. [24] In recent years, BODIPY derivatives are also being explored as photosensitizers for applications in photodynamic therapy [25] and photocatalysis. [26]



Related Research Articles

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A heterocyclic compound or ring structure is a cyclic compound that has atoms of at least two different elements as members of its ring(s). Heterocyclic organic chemistry is the branch of organic chemistry dealing with the synthesis, properties, and applications of organic heterocycles.

Pyrrole is a heterocyclic, aromatic, organic compound, a five-membered ring with the formula C4H4NH. It is a colorless volatile liquid that darkens readily upon exposure to air. Substituted derivatives are also called pyrroles, e.g., N-methylpyrrole, C4H4NCH3. Porphobilinogen, a trisubstituted pyrrole, is the biosynthetic precursor to many natural products such as heme.

<span class="mw-page-title-main">Fluorophore</span> Agents that emit light after excitation by light

A fluorophore is a fluorescent chemical compound that can re-emit light upon light excitation. Fluorophores typically contain several combined aromatic groups, or planar or cyclic molecules with several π bonds.

<span class="mw-page-title-main">Phthalocyanine</span> Chemical compound

Phthalocyanine is a large, aromatic, macrocyclic, organic compound with the formula (C8H4N2)4H2 and is of theoretical or specialized interest in chemical dyes and photoelectricity.

Cyanines, also referred to as tetramethylindo(di)-carbocyanines are a synthetic dye family belonging to the polymethine group. Although the name derives etymologically from terms for shades of blue, the cyanine family covers the electromagnetic spectrum from near IR to UV.

Phosphole is the organic compound with the chemical formula C
4H
4PH; it is the phosphorus analog of pyrrole. The term phosphole also refers to substituted derivatives of the parent heterocycle. These compounds are of theoretical interest but also serve as ligands for transition metals and as precursors to more complex organophosphorus compounds.

<span class="mw-page-title-main">Boronic acid</span> Organic compound of the form R–B(OH)2

A boronic acid is an organic compound related to boric acid in which one of the three hydroxyl groups is replaced by an alkyl or aryl group. As a compound containing a carbon–boron bond, members of this class thus belong to the larger class of organoboranes.

<span class="mw-page-title-main">Squaraine dye</span> Class of organic molecules

Squaraine dyes are a class of organic dyes showing intense fluorescence, typically in the red and near infrared region. They are characterized by their unique aromatic four membered ring system derived from squaric acid. Most squaraines are encumbered by nucleophilic attack of the central four membered ring, which is highly electron deficient. This encumbrance can be attenuated by the formation of a rotaxane around the dye to protect it from nucleophiles. They are currently used as sensors for ions and have recently, with the advent of protected squaraine derivatives, been exploited in biomedical imaging.

<span class="mw-page-title-main">Metallole</span>

Metalloles are metallacycle derivatives of cyclopentadiene in which the carbon atom at position 5, the saturated carbon, is replaced by a heteroatom. In contrast to its parent compound, the numbering of the metallole starts at the heteroatom. Some of these compounds are described as organometallic compounds, but in the list below quite a number of metalloids are present too. Many metalloles are fluorescent. Polymeric derivatives of pyrrole and thiophene are of interest in molecular electronics. Metalloles, which can also be viewed as structural analogs of pyrrole, include:

<span class="mw-page-title-main">Tetraphenylporphyrin</span> Chemical compound

Tetraphenylporphyrin, abbreviated TPP or H2TPP, is a synthetic heterocyclic compound that resembles naturally occurring porphyrins. Porphyrins are dyes and cofactors found in hemoglobin and cytochromes and are related to chlorophyll and vitamin B12. The study of naturally occurring porphyrins is complicated by their low symmetry and the presence of polar substituents. Tetraphenylporphyrin is hydrophobic, symmetrically substituted, and easily synthesized. The compound is a dark purple solid that dissolves in nonpolar organic solvents such as chloroform and benzene.

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<span class="mw-page-title-main">Porphyrazine</span> Chemical compound

Porphyrazines, or tetraazaporphyrins, are tetrapyrrole macrocycles similar to porphyrins and phthalocyanines. Pioneered by Sir R. Patrick Linstead as an extension of his work on phthalocyanines, porphyrazines differ from porphyrins in that they contain -meso nitrogen atoms, rather than carbon atoms, and differ from phthalocyanines in that their β-pyrrole positions are open for substitution. These differences confer physical properties that are distinct from both porphyrins and phthalocyanines.

<span class="mw-page-title-main">Carbon quantum dot</span> Type of carbon nanoparticle

Carbon quantum dots also commonly called carbon nano dots are carbon nanoparticles which are less than 10 nm in size and have some form of surface passivation.

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<span class="mw-page-title-main">1,3-Diphenylisobenzofuran</span> Chemical compound

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Boron porphyrins are a variety of porphyrin, a common macrocycle used for photosensitization and metal trapping applications, that incorporate boron. The central four nitrogen atoms in a porphyrin macrocycle form a unique molecular pocket which is known to accommodate transition metals of various sizes and oxidation states. Due to the diversity of binding modes available to porphyrin, there is a growing interest in introducing other elements into this pocket.

<span class="mw-page-title-main">2,2'-Dipyrromethene</span> Chemical compound

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9H
8N
2 whose skeleton can be described as two pyrrole rings C
5N connected by a methyne bridge =CH– through their nitrogen-adjacent (position-2) carbons; the remaining bonds being satisfied by hydrogen atoms. It is an unstable compound that is readily attacked by nucleophilic compounds above −40 °C.

<span class="mw-page-title-main">Borepin</span> Aromatic, boron-containing rings

Borepins are a class of boron-containing heterocycles used in main group chemistry. They consist of a seven-membered unsaturated ring with a tricoordinate boron in it. Simple borepins are analogues of cycloheptatriene, which is a seven-membered ring containing three carbon-carbon double bonds, each of which contributes 2π electrons for a total of 6π electrons. Unlike other seven-membered systems such as silepins and phosphepins, boron has a vacant p-orbital that can interact with the π and π* orbitals of the cycloheptatriene. This leads to an isoelectronic state akin to that of the tropylium cation, aromatizing the borepin while also allowing it to act as a Lewis acid. The aromaticity of borepin is relatively weak compared to traditional aromatics such as benzene or even cycloheptatriene, which has led to the synthesis of many fused, π-conjugated borepin systems over the years. Simple and complex borepins have been extensively studied more recently due to their high fluorescence and potential applications in technologies like organic light-emitting diodes (OLEDs) and photovoltaic cells.

<span class="mw-page-title-main">Boraacenes</span> Boron containing acene compounds

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References

  1. 1 2 3 4 5 6 7 8 9 10 11 K. Tram; H. Yan; H. A. Jenkins; S. Vassiliev; D. Bruce (2009). "The synthesis and crystal structure of unsubstituted 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY)". Dyes and Pigments. 82 (3): 392–395. doi:10.1016/j.dyepig.2009.03.001.
  2. 1 2 A. Schmitt; B. Hinkeldey; M. Wild; G. Jung (2009). "Synthesis of the Core Compound of the BODIPY Dye Class: 4,4′-Difluoro-4-bora-(3a,4a)-diaza-s-indacene". J. Fluoresc. 19 (4): 755–759. doi:10.1007/s10895-008-0446-7. PMID   19067126. S2CID   7012021.
  3. ↑ I. J. Arroyo; R. Hu; G. Merino; B. Z. Tang; E. Peña-Cabrera (2009). "The Smallest and One of the Brightest. Efficient Preparation and Optical Description of the Parent Borondipyrromethene System". J. Org. Chem. 74 (15): 5719–22. doi:10.1021/jo901014w. PMID   19572588.
  4. ↑ Alfred Treibs und Franz-Heinrich Kreuzer. Difluorboryl-Komplexe von Di- und Tripyrrylmethenen. Justus Liebigs Annalen der Chemie 1968, 718 (1): 208-223. doi: 10.1002/jlac.19687180119
  5. 1 2 3 4 Burgess, Kevin (October 2007). "BODIPY Dyes and Their Derivatives: Syntheses and Spectroscopic Properties". Chemical Reviews. 107 (11): 4891–4932. doi:10.1021/cr078381n. PMID   17924696.
  6. 1 2 3 Groves, Brandon R.; Crawford, Sarah M.; Lundrigan, Travis; Matta, Chérif F.; Sowlati-Hashjin, Shahin; Thompson, Alison (2013). "Synthesis and characterisation of the unsubstituted dipyrrin and 4,4-dichloro-4-bora-3a,4a-diaza-s-indacene: Improved synthesis and functionalisation of the simplest BODIPY framework". Chem. Commun. 49 (8): 816–818. doi:10.1039/c2cc37480c. PMID   23235887.
  7. 1 2 Aurore Loudet and Kevin Burgess (2007): "BODIPY dyes and their derivatives:  Syntheses and spectroscopic properties". Chemical Reviews, volume 107, issue 11, pages 4891–4932. doi : 10.1021/cr078381n
  8. ↑ Zhong-Hua Pan; Geng-Geng Luo; Jing-Wei Zhou; Jiu-Xu Xia; Kai Fang; Rui-Bo Wu (2014). "A simple BODIPY-aniline-based fluorescent chemosensor as multiple logic operations for the detection of pH and CO2 gas". Dalton Transactions. 43 (22): 8499–507. doi:10.1039/C4DT00395K. PMID   24756338.
  9. ↑ Stachelek, Patrycja; Alsimaree, Abdulrahman A.; Alnoman, Rua B.; Harriman, Anthony; Knight, Julian G. (2017-03-16). "Thermally-Activated, Delayed Fluorescence in O,B,O- and N,B,O-Strapped Boron Dipyrromethene Derivatives". The Journal of Physical Chemistry A. 121 (10): 2096–2107. Bibcode:2017JPCA..121.2096S. doi:10.1021/acs.jpca.6b11131. ISSN   1089-5639. PMID   28245114.
  10. ↑ Sirbu, Dumitru; Benniston, Andrew C.; Harriman, Anthony (2017-04-07). "One-Pot Synthesis of a Mono-O,B,N-strapped BODIPY Derivative Displaying Bright Fluorescence in the Solid State". Organic Letters. 19 (7): 1626–1629. doi:10.1021/acs.orglett.7b00435. ISSN   1523-7060. PMID   28319396.
  11. ↑ Lu, Hua; Mack, John; Yang, Yongchao; Shen, Zhen (2014). "Structural modification strategies for the rational design of red/NIR region BODIPYs". Chem. Soc. Rev. 43 (13): 4778–4823. doi:10.1039/C4CS00030G. ISSN   0306-0012. PMID   24733589.
  12. ↑ Wang, Dongchuan; Fan, Jiangli; Gao, Xinqin; Wang, Bingshuai; Sun, Shiguo; Peng, Xiaojun (2009-10-16). "Carboxyl BODIPY Dyes from Bicarboxylic Anhydrides: One-Pot Preparation, Spectral Properties, Photostability, and Biolabeling". The Journal of Organic Chemistry. 74 (20): 7675–7683. doi:10.1021/jo901149y. ISSN   0022-3263. PMID   19772337.
  13. ↑ Perronet, K.; Bouyer, P.; Westbrook, N.; Soler, N.; Fourmy, D.; Yoshizawa, S. (November 2007). "Single molecule fluorescence detection of BODIPY-FL molecules for monitoring protein synthesis". Journal of Luminescence. 127 (1): 264–268. Bibcode:2007JLum..127..264P. doi:10.1016/j.jlumin.2007.02.051.
  14. ↑ Cooper, Mark S.; Szeto, Daniel P.; Sommers-Herivel, Greg; Topczewski, Jacek; Solnica-Krezel, Lila; Kang, Hee-Chol; Johnson, Iain; Kimelman, David (February 2005). "Visualizing morphogenesis in transgenic zebrafish embryos using BODIPY TR methyl ester dye as a vital counterstain for GFP". Developmental Dynamics. 232 (2): 359–368. doi: 10.1002/dvdy.20252 . ISSN   1058-8388. PMID   15614774.
  15. ↑ Guseva, Galina B.; Antina, Elena V.; Berezin, Mikhail B.; Ksenofontov, Alexander A.; Bocharov, Pavel S.; Smirnova, Anastassia S.; Pavelyev, Roman S.; Gilfanov, Ilmir R.; Pestova, Svetlana V.; Izmest'ev, Evgeny S.; Rubtsova, Svetlana A.; Kayumov, Airat R.; Kiselev, Sergei V.; Azizova, Zulfiya R.; Ostolopovskaya, Olga V. (March 2022). "Conjugate of meso-carboxysubstituted-BODIPY with thioterpenoid as an effective fluorescent probe: Synthesis, structure, spectral characteristics, and molecular docking". Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 268: 120638. Bibcode:2022AcSpA.26820638G. doi:10.1016/j.saa.2021.120638. PMID   34840052. S2CID   244408920.
  16. ↑ Kaufman, Nichole E. M.; Meng, Qianli; Griffin, Kaitlin E.; Singh, Sitanshu S.; Dahal, Achyut; Zhou, Zehua; Fronczek, Frank R.; Mathis, J. Michael; Jois, Seetharama D.; Vicente, M. Graça H. (2019-04-11). "Synthesis, Characterization, and Evaluation of Near-IR Boron Dipyrromethene Bioconjugates for Labeling of Adenocarcinomas by Selectively Targeting the Epidermal Growth Factor Receptor". Journal of Medicinal Chemistry. 62 (7): 3323–3335. doi:10.1021/acs.jmedchem.8b01746. ISSN   0022-2623. PMC   6693348 . PMID   30835998.
  17. ↑ Sirbu, Dumitru; Luli, Saimir; Leslie, Jack; Oakley, Fiona; Benniston, Andrew C. (2019-05-17). "Enhanced in vivo Optical Imaging of the Inflammatory Response to Acute Liver Injury in C57BL/6 Mice Using a Highly Bright Near-Infrared BODIPY Dye". ChemMedChem. 14 (10): 995–999. doi:10.1002/cmdc.201900181. ISSN   1860-7179. PMID   30920173. S2CID   85544665.
  18. ↑ Kowada, Toshiyuki; Maeda, Hiroki; Kikuchi, Kazuya (2015). "BODIPY-based probes for the fluorescence imaging of biomolecules in living cells". Chemical Society Reviews. 44 (14): 4953–4972. doi:10.1039/C5CS00030K. PMID   25801415.
  19. ↑ Ni, Yong; Wu, Jishan (2014). "Far-red and near infrared BODIPY dyes: Synthesis and applications for fluorescent pH probes and bio-imaging". Organic & Biomolecular Chemistry. 12 (23): 3774–91. doi:10.1039/c3ob42554a. PMID   24781214.
  20. ↑ Abrahamse, Heidi; Hamblin, Michael R. (2016). "New photosensitizers for photodynamic therapy". Biochemical Journal. 473 (4): 347–364. doi:10.1042/BJ20150942. PMC   4811612 . PMID   26862179.
  21. ↑ Lu, Hua; Mack, John; Yang, Yongchao; Shen, Zhen (2014). "Structural modification strategies for the rational design of red/NIR region BODIPYs". Chem. Soc. Rev. 43 (13): 4778–4823. doi:10.1039/C4CS00030G. PMID   24733589.
  22. ↑ Roncali, Jean (2009). "Molecular Bulk Heterojunctions: An Emerging Approach to Organic Solar Cells". Accounts of Chemical Research. 42 (11): 1719–1730. doi:10.1021/ar900041b. PMID   19580313.
  23. ↑ Kim, Ha Na; Ren, Wen Xiu; Kim, Jong Seung; Yoon, Juyoung (2012). "Fluorescent and colorimetric sensors for detection of lead, cadmium, and mercury ions". Chem. Soc. Rev. 41 (8): 3210–3244. doi:10.1039/C1CS15245A. PMID   22184584.
  24. ↑ Kosswattaarachchi, Anjula M.; Friedman, Alan E.; Cook, Timothy R. (2016). "Characterization of a BODIPY Dye as an Active Species for Redox Flow Batteries". ChemSusChem. 9 (23): 3317–3323. Bibcode:2016ChSCh...9.3317K. doi:10.1002/cssc.201601104. PMID   27863048.
  25. ↑ Turksoy, Abdurrahman; Yildiz, Deniz; Akkaya, Engin U. (2019-01-15). "Photosensitization and controlled photosensitization with BODIPY dyes". Coordination Chemistry Reviews. Novel and Smart Photosensitizers from Molecule to Nanoparticle. 379: 47–64. doi:10.1016/j.ccr.2017.09.029. hdl: 11693/52868 . ISSN   0010-8545. S2CID   104018445.
  26. ↑ De Bonfils, Paul; Péault, Louis; Nun, Pierrick; Coeffard, Vincent (2021-03-26). "State of the Art of Bodipy-Based Photocatalysts in Organic Synthesis". European Journal of Organic Chemistry. 2021 (12): 1809–1824. doi:10.1002/ejoc.202001446. ISSN   1434-193X. S2CID   233683967.
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