A Simple Central Seven-Membered BOPYIN: Synthesis,Structural, Spectroscopic Properties,and Cellular Imaging Application

A two-step, one-flask synthesis of central seven-membered borondifluoride-3,3-dimethyl-2-[2-(2-pyrrolyl)ethenyl] indole (BOPYIN) ligands has been developed by using the unexplored 3,3-dimethyl-2-[2-(2-pyrrolyl)ethenyl] indole. The simple synthetic approach has enabled modification of the electronic structure by changing the substituents on the indole unit. X-ray analysis indicated that conformations of the seven-membered BF₂ complex including BOPYIN and diazaborepin differ from that of the five- and six-membered organoboron complexes. Interestingly, the bond angle of the N⋅⋅⋅B−N bond increases with the number of atoms in the core ring, based on Baeyer strain theory. These unsymmetric BOPYIN derivatives have excellent photophysical properties, including high fluorescence quantum yields, except for BOPYIN- 4 in the solution state, large Stokes shifts, and good molar absorptivity. The dipole moment of BOPYIN- 3 in the first excited singlet state and ground state was demonstrated by a linear Lippert–Mataga plot. The absorption and emission spectra were not mirror images for BOPYIN- 1 – 3 and 5 , in contradiction to Kasha's rule, as determined by TDDFT. The synthesized BOPYINs have been shown to be biocompatible fluorophores in cell bioimaging.     

Pyrrolopyrrole Cyanine Dyes: A New Class of Near‐Infrared Dyes and Fluorophores

NIRer there : Pyrrolopyrrole cyanine (PPCys) dyes, a new class of near‐infrared (NIR) fluorophores, are obtained by condensation of heteroarylacetonitrile and diketopyrrolopyrrole compounds (see picture). Complexation with BF₂ or BPh₂ yields strongly fluorescent, photostable NIR dyes that show high absorption cross‐sections and fluorescence quantum yields. Furthermore, alteration of the heterocycle can tune the main absorption between λ = 684 and 864 nm.

     

Synthesis and Molecular Properties of Acceptor‐Substituted Squaraine Dyes

A broad series of more than 20 acceptor‐substituted squaraines was synthesized that feature different acceptor functionalities at the central squaraine four‐membered ring. The influence of these acceptor units on the reactivity of semisquaraine precursors and stability of the respective squaraines were explored. Thereby the dicyanovinyl group was found to be the most versatile acceptor group that enabled various modifications at the donor moiety of the squaraine scaffold, leading to an extended series of dicyanovinyl‐functionalized squaraines. The variation of donor units afforded a set of NIR fluorophores that cover a wavelength region from the visible at about 650 nm far into the NIR up to 920 nm with fluorescence quantum yields between 0.93 and 0.11 and outstanding optical brightness. This excellent optical property is related to a rigid molecular scaffold that is fixed in an all‐cis configuration by the additional dicyanovinyl acceptor unit. The change of the molecular symmetry from C_2h to C_2v upon functionalization of the squaraine core with dicyanovinyl acceptor group has been confirmed in solution by electro‐optical absorption (EOA) spectroscopy, revealing permanent ground‐state dipole moments μ_g in the range between 4.3 and 6.4 D. These dipole moments direct an antiparallel packing of the molecules in the solid state according to single‐crystal X‐ray analyses achieved for four dicyanovinyl‐functionalized squaraines. The structural properties, the EOA results, as well as the band shapes of the optical spectra indicate that these polymethine dyes are cyanine‐type chromophores. It is worth noting that the orientation of the dipole moment vectors is orthogonal to the orientation of the transition dipole moment vectors, which is an uncommon but characteristic feature of this rather novel class of polymethine dyes. With regard to applications of these dyes in organic solar cells, their redox properties were also studied by cyclic voltammetry.     

Synthesis of Symmetrical Multichromophoric Bodipy Dyes and Their Facile Transformation into Energy Transfer Cassettes

Multichromophoric boron‐dipyrromethene (Bodipy) dyes synthesized on phenylene‐ethynylene platforms have been be converted to energy transfer cassettes in a one‐step chemical transformation. Excitation energy transfer processes in these highly symmetrical derivatives were studied in detail, including time‐resolved fluorescence spectroscopy techniques. Excitation spectra and the emission lifetimes suggest efficient energy transfer between the donor and acceptor chromophore. These novel energy transfer cassettes, while highlighting a short‐cut approach to similar energy transfer systems, could be useful as large pseudo‐Stokes shift multichromophoric dyes with potential applications in diverse applications.     

Comparative Photostability Studies of BODIPY and Fluorescein Dyes by Using Fluorescence Correlation Spectroscopy

In single‐molecule applications, the photostability of fluorescent molecules is a key parameter. We apply fluorescence correlation spectroscopy to compare the photostability of four fluorescein and four borondipyrromethene (BODIPY) dyes of similar structure but different triplet yields. The latter class of dyes are more stable. In the kinetic analysis the, diffusion and photobleaching are treated as competitive processes. Corrections, which account for saturation and for experimental artefacts, are achieved solely by using experimental data. Photobleaching is found to occur mainly through the first excited singlet state S₁, in contrast to previous findings.     

New Fluorinated Rhodamines for Optical Microscopy and Nanoscopy

New photostable rhodamine dyes represented by the compounds 1 a – r and 3 – 5 are proposed as efficient fluorescent markers with unique combination of structural features. Unlike rhodamines with monoalkylated nitrogen atoms, N′,N‐bis(2,2,2‐trifluoroethyl) derivatives 1 e , 1 i , 1 j , 3 ‐H and 5 were found to undergo sulfonation of the xanthene fragment at the positions 4′ and 5′. Two fluorine atoms were introduced into the positions 2′ and 7′ of the 3′,6′‐diaminoxanthene fragment in compounds 1 a – d , 1 i – l and 1 m – r . The new rhodamine dyes may be excited with λ=488 or 514 nm light; most of them emit light at λ=512–554 nm (compounds 1 q and 1r at λ=576 and 589 nm in methanol, respectively) and have high fluorescence quantum yields in solution (up to 98 %), relatively long excited‐state lifetimes (>3 ns) and are resistant against photobleaching, especially at high laser intensities, as is usually applied in confocal microscopy. Sulfonation of the xanthene fragment with 30 % SO₃ in H₂SO₄ is compatible with the secondary amide bond (rhodamine‐CON(Me)CH₂CH₂COOH) formed with MeNHCH₂CH₂COOCH₃ to providing the sterically unhindered carboxylic group required for further (bio)conjugation reactions. After creating the amino reactive sites, the modified derivatives may be used as fluorescent markers and labels for (bio)molecules in optical microscopy and nanoscopy with very‐high light intensities. Further, the new rhodamine dyes are able to pass the plasma membrane of living cells, introducing them as potential labels for recent live‐cell‐tag approaches. We exemplify the excellent performance of the fluorinated rhodamines in optical microscopy by fluorescence correlation spectroscopy (FCS) and stimulated emission depletion (STED) nanoscopy experiments.     

Conformationally restricted dipyrromethene boron difluoride (BODIPY) dyes: highly fluorescent, multicolored probes for cellular imaging

Novel fluorescent, conformationally restricted dipyrromethene boron difluoride (BODIPY) dyes have been prepared by introducing a naphthalenyl group at the meso position of the BODIPY core. These BODIPY dyes exhibit increased fluorescence quantum yields compared with dyes that have a meso-position phenyl group with internal rotation. The absorption and emission wavelengths of such conformationally restricted BODIPY dyes can be easily tuned to the near-IR range by derivatization through a condensation reaction with benzaldehyde derivatives. The two-photon absorption properties of these BODIPY dyes were also investigated and the results show that they exhibit increased two-photon excited fluorescence compared to analogue dyes that contain a phenyl group. The one- and two-photon fluorescence imaging of living cells by using selected BODIPY dyes has been successfully demonstrated.     

Highly Fluorescent and Water‐Soluble Diketopyrrolopyrrole Dyes for Bioconjugation

The preparation of highly water‐soluble and strongly fluorescent diketopyrrolopyrrole (DPP) dyes using an unusual taurine‐like sulfonated linker has been achieved. Exchanging a phenyl for a thienyl substituent shifts the emission wavelength to near λ=600 nm. The free carboxylic acid group present in these new derivatives was readily activated and the dyes were subsequently covalently linked to a model protein (bovine serum albumin; BSA). The bioconjugates were characterized by electronic absorption, fluorescence spectroscopy and MALDI‐TOF mass spectrometry, thus enabling precise determination of the labeling density (ratio DPP/BSA about 3 to 8). Outstanding values of fluorescence quantum yield (30 % to 59 %) for these bioconjugates are obtained. The photostability of these DPP dyes is considerably greater than that of fluorescein under the same irradiation conditions. Remarkably low detection limits between 80 and 300 molecules/μm² were found for the BSA bioconjugates by fluorescence imaging with a epifluorescence microscope.     

Dihydronaphthalene‐Fused Boron–Dipyrromethene (BODIPY) Dyes: Insight into the Electronic and Conformational Tuning Modes of BODIPY Fluorophores

A new series of boron–dipyrromethene (BDP, BODIPY) dyes with dihydronaphthalene units fused to the β‐pyrrole positions ( 1 a – d , 2 ) has been synthesised and spectroscopically investigated. All the dyes, except pH‐responsive 1 d in polar solvents, display intense emission between 550–700 nm. Compounds 1 a and 1 b with a hydrogen atom and a methyl group in the meso position of the BODIPY core show spectroscopic properties that are similar to those of rhodamine 101, thus rendering them potent alternatives to the positively charged rhodamine dyes as stains and labels for less polar environments or for the dyeing of latex beads. Compound 1 d , which carries an electron‐donating 4‐(dimethylamino)phenyl group in the meso position, shows dual fluorescence in solvents more polar than dibutyl ether and can act as a pH‐responsive “light‐up” probe for acidic pH. Correlation of the pK_a data of 1 d and several other meso‐(4‐dimethylanilino)‐substituted BODIPY derivatives allowed us to draw conclusions on the influence of steric crowding at the meso position on the acidity of the aniline nitrogen atom. Preparation and investigation of 2 , which carries a nitrogen instead of a carbon as the meso‐bridgehead atom, suggests that the rules of colour tuning of BODIPYs as established so far have to be reassessed; for all the reported couples of meso‐C‐ and meso‐N‐substituted BODIPYs, the exchange leads to pronounced redshifts of the spectra and reduced fluorescence quantum yields. For 2 , when compared with 1 a , the opposite is found: negligible spectral shifts and enhanced fluorescence. Additional X‐ray crystallographic analysis of 1 a and quantum chemical modelling of the title and related compounds employing density functional theory granted further insight into the features of such sterically crowded chromophores.     

Sterically Shielded Heptamethine Cyanine Dyes for Bioconjugation and High Performance Near-Infrared Fluorescence Imaging

The near-infrared window of fluorescent heptamethine cyanine dyes greatly facilitates biological imaging because there is deep penetration of the light and negligible background fluorescence. However, dye instability, aggregation, and poor pharmacokinetics are current drawbacks that limit performance and the scope of possible applications. All these limitations are simultaneously overcome with a new molecular design strategy that produces a charge balanced and sterically shielded fluorochrome. The key design feature is a meso-aryl group that simultaneously projects two shielding arms directly over each face of a linear heptamethine polyene. Cell and mouse imaging experiments compared a shielded heptamethine cyanine dye (and several peptide and antibody bioconjugates) to benchmark heptamethine dyes and found that the shielded systems possess an unsurpassed combination of photophysical, physiochemical, and biodistribution properties that greatly enhance bioimaging performance.     

Ultrafast Photoinduced Electron Transfer in Viologen‐Linked BODIPY Dyes

New boron‐dipyrromethene (BODIPY) dyes linked to viologen are prepared and their photophysical and electrochemical properties are investigated. Both synthesized molecules have similar electronic absorption spectra with the absorption maximum localized at 517 and 501 nm for dye 1 and dye 2 , respectively. They exhibit well‐defined redox behavior, highlighting the presence of BODIPY and viologen subunits, with little perturbation of the redox potential of both subunits with respect to the parent compounds. Both dyes are heavily quenched by photoinduced electron transfer from the BODIPY to the viologen subunit. The transient absorption technique demonstrates that dye 2 forms the viologen radical within a timeframe of 7.1 ps, and that the charge‐separated species has a lifetime of 59 ps. Sustained irradiation of dye 2 in the presence of a tertiary amine allows for the accumulation of BODIPY–methyl‐4,4′‐bipyridinium (BODIPY–MV⁺), as observed by its characteristic absorption at 396 and 603 nm. However, dye 2 does not generate catalytic amounts of hydrogen under standard conditions.     

Tuning the Solid‐State Luminescence of BODIPY Derivatives with Bulky Arylsilyl Groups: Synthesis and Spectroscopic Properties

Boron dipyrromethenes (BODIPYs) with bulky triphenylsilylphenyl(ethynyl) and triphenylsilylphenyl substituents on pyrrole sites were prepared via Hagihara–Sonogashira and Suzuki–Miyaura cross‐coupling with ethynyl‐terminated tetraphenylsilane and boronic acid‐terminated tetraphenylsilane. The chromophores are designed to prevent intermolecular π–π stacking interaction and enhance fluorescence in the solid state. Single crystals of 1 a and 2 b for X‐ray structural analysis were obtained, and weak π–π stacking interactions of the neighboring BODIPY molecules were observed. Spectroscopic properties of all of the dyes in various solvents and in films were investigated. Triphenylsilylphenyl‐substituted BODIPYs generally show more pronounced increases in solid‐state emission than triphenylsilylphenyl(ethynyl)‐substituted BODIPYs. Although the simple BODIPYs do not exhibit any fluorescence in the solid state (Φ=0), arylsilyl‐substituted BODIPYs exhibit weak to moderate solid‐state fluorescence with quantum yields of 0.03, 0.07, 0.10, and 0.25. The structure–property relationships were analyzed on the basis of X‐ray crystallography, optical spectroscopy, cyclic voltammetry, and theoretical calculations.     

Monofluorination and Trifluoromethylation of BODIPY Dyes for Prolonged Single‐Molecule Detection

Electrophilic monofluorination with Selectfluor and nucleophilic trifluoromethylation with the Ruppert–Prakesh reagent of dimethyl‐, tetramethyl‐ and pentamethyl‐substituted boron dipyrromethenes (BODIPY) are investigated. Monofluorinated dyes are synthesized with low yields (<30 %), however trifluoromethyl derivatives are obtained in moderate to high yields (≈40–90 %). All compounds are characterized by steady‐state and time‐resolved fluorescence spectroscopy, the photostability is investigated with fluorescence correlation spectroscopy (FCS) and total internal reflection fluorescence microscopy (TIRF). Monofluorination hardly affects the spectroscopic parameters of the unsubstituted parent compounds, but distinctly enhances the photostability, whereas trifluoromethylation leads to a hypsochromic shift by up to 17 nm in both absorption and emission, slightly enhanced intersystem crossing, and higher photostability. Further development of soft fluorination and trifluoromethylation methods is therefore highly desired.     

Sterically Shielded Heptamethine Cyanine Dyes for Bioconjugation and High Performance Near‐Infrared Fluorescence Imaging

The near‐infrared window of fluorescent heptamethine cyanine dyes greatly facilitates biological imaging because there is deep penetration of the light and negligible background fluorescence. However, dye instability, aggregation, and poor pharmacokinetics are current drawbacks that limit performance and the scope of possible applications. All these limitations are simultaneously overcome with a new molecular design strategy that produces a charge balanced and sterically shielded fluorochrome. The key design feature is a meso‐aryl group that simultaneously projects two shielding arms directly over each face of a linear heptamethine polyene. Cell and mouse imaging experiments compared a shielded heptamethine cyanine dye (and several peptide and antibody bioconjugates) to benchmark heptamethine dyes and found that the shielded systems possess an unsurpassed combination of photophysical, physiochemical, and biodistribution properties that greatly enhance bioimaging performance.     

Near‐IR BODIPY Dyes à la Carte—Programmed Orthogonal Functionalization of Rationally Designed Building Blocks

Herein, we report the synthesis of polyfunctional BODIPY building blocks suitable to be subjected to several reaction sequences with complete chemoselectivity, thereby allowing the preparation of complex BODIPY derivatives in a versatile and programmable manner. The reactions included the Liebeskind–Srogl cross‐coupling reaction (LSCC), nucleophilic aromatic substitution (S_NAr), Suzuki, Sonogashira, and Stille couplings, and a desulfitative reduction of the MeS group. This novel synthetic protocol is a powerful route to design a library of compounds with tailored photophysical properties for advanced applications. In this context, it is noteworthy that it offers a straightforward and cost‐effective strategy to shift the BODIPY emission deep into the near‐infrared spectral region while retaining high fluorescence quantum yields as well as highly efficient and stable laser action. These new dyes outperform the lasing behaviour of dyes considered as benchmarks over the red spectral region, overcoming the important drawbacks associated with these commercial laser dyes, namely low absorption at the standard pump wavelengths (355 and 532 nm) and/or poor photostability.     

Silyl‐ and Disilanyl‐BODIPYs: Synthesis via Catalytic Dehalosilylation and Spectroscopic Properties

We describe herein the first synthesis of silyl‐ and disilanyl‐BODIPYs through transition‐metal‐catalyzed dehalosilylation of iodo‐BODIPYs using a Pd(P(t Bu)₃)₂/Et₃N/toluene system. Various mono‐ and bis‐silyl‐BODIPYs, mono‐ and bis‐disilanyl‐BODIPYs and bis‐BODIPYs linked by silylene and SiOSi groups were synthesized by using this straightforward method. Silyl‐ and disilanyl‐substitution significantly modifies the spectroscopic properties of the BODIPY, in which the fluorescence quantum yields of the silyl‐BODIPYs are remarkably increased, whereas the emission spectra of disilanyl‐BODIPYs are red‐shifted due to effective σ(SiSi)–π(BODIPY) conjugation.