Dyes in modern organic chemistry
Dye chemistry is a traditional and highly interdisciplinary research area in organic chemistry. Specifically, the synthesis, experimental and theoretical investigation, as well as the application of organic dyes contribute significantly to several disciplines in chemistry. In this context, recent progress in organic synthesis and highly sophisticated physical–chemical or analytical methods led to a renaissance of dye chemistry; as specifically designed dyes are required to fulfil the special requirements to be employed in, for example, high-resolution microscopy, fluorescence spectroscopy, photovoltaics or OLED materials. Hence, this thematic issue of the Beilstein Journal of Organic Chemistry aims to cover the diverse modern aspects of organic dye chemistry that range from the traditional disciplines, namely synthesis and investigation of photophysical properties, to applications in spectroscopy, sensing, (bio)analytical chemistry, materials science, biology, and industry.
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- Published 25 Mar 2019
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Scheme 1: Approach of the direct azologization of reported [60,61] serotonin 5-HT3R antagonists via replacement of a...
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Scheme 2: Synthesis of the differently substituted quinoxaline azobenzene derivatives 5a and 5b via Baeyer [62]–M...
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Scheme 3: Synthesis of the methoxy-substituted quinoxaline derivative 12a via diazotization [66-69].
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Scheme 4: General procedure for the synthesis of purine- and thienopyrimidine-substituted arylazobenzenes and...
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Scheme 5: Synthesis of the thiomethyl-linked purine azobenzene 23 [62,63,72-74].
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Scheme 6: Synthesis of the amide-linked azobenzene purine 28 [62,63,75-77].
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Figure 1: UV–vis absorption spectra measured at 50 µM in DMSO. Left: purine derivative 16c; right: azo-extend...
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Figure 2: On the left panel representative traces of currents induced by the application of 3 µM 5HT (black t...
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- Published 26 Apr 2019
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Figure 1: Bifunctional DAT as a cross-linker for proteins. The compound is a turn-on-probe, i.e., the fluores...
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Scheme 1: Preparation of DAT–ALA conjugate 3 with fluorinated benzyl residue.
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Scheme 2: Preparation of conjugate 7 consisting of fluorinated DAT and ALA moieties with an additional propyl...
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Figure 2: High-resolution XPS of SAM 3.
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Figure 3: High-resolution XPS of SAM 7.
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- Published 06 Jun 2019
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Figure 1: BN-phenanthrene 1a and synthesis of substituted derivatives proposed in this work.
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Scheme 1: Synthesis of Cl-substituted BN-phenanthrene 1b.
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Scheme 2: Palladium-catalyzed cross-couplings of Cl-substituted BN-phenanthrene 1b.
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Scheme 3: Pd-catalyzed Sonogashira reactions of Cl-substituted BN-phenanthrene 1b.
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Figure 2: UV–vis absorption (top) and emission (bottom) spectra for BN-phenanthrenes 1 and 5 in cyclohexane (...
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Figure 3: Solutions of 1a–f and 5 (from left to right) under UV irradiation.
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- Published 24 Jun 2019
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Figure 1: Heterotriacenes DTT 1, DTS 2, DST 3, and DSS 4 with varying number of selenium atoms and fused sele...
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Scheme 1: Synthesis of heterotriacenes DTT 1 and DTS 2 via copper-catalyzed cross-coupling reactions.
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Scheme 2: Synthesis of selenolotriacenes DST 3 and DSS 4.
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Figure 2: Single crystal X-ray structure analysis of selenolotriacene DST 3, (a) individual molecule and atom...
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Figure 3: Single crystal X-ray structure analysis of selenolotriacene DST 3: (a) partial overlap of stacked a...
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Figure 4: DFT quantum chemical calculated geometry of DTT 1 and general atom labelling for all heterotriacene...
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Figure 5: Representative electron density of frontier orbitals LUMO, HOMO, and HOMO-1 for heterotriacene DSS 4...
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Figure 6: Normalized absorption spectra of heteroacenes DTT 1 (black line), DTS 2 (blue line), DST 3 (green l...
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Figure 7: Energy diagram of the frontier molecular orbitals of heterotriacenes 1–4.
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Figure 8: Multisweep voltammograms for the electrochemical polymerization of monomeric heterotriacene DST 2 i...
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Scheme 3: Oxidative polymerization of heterotriacenes 1–4 to corresponding conjugated polymers P1–P4.
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- Published 22 Jul 2019
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Figure 1: Chemical structures of the (D–π–)2A fluorescent dyes OUY-2, OUK-2 and OUJ-2.
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Scheme 1: Synthesis of OUY-2, OUK-2 and OUJ-2.
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Figure 2: (a) Photoabsorption and (b) fluorescence (λex = ca. 400 nm) spectra of OUY-2 in various solvents. (...
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Figure 3: Correlation of the Stokes shift (νst) and the orientation polarizability (Δf) according to Equation 1 and Equation 2, r...
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Figure 4: Fluorescence spectra of OUY-2 (λex = 370 nm), OUK-2 (λex = 370 nm) and OUJ-2 (λex = 380 nm) in the ...
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Figure 5: Cyclic voltammograms of OUY-2, OUK-2 and OUJ-2 in DMF containing 0.1 M Bu4NClO4. The arrow denotes ...
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Figure 6: Energy level diagram, HOMO and LUMO of OUY-2, OUK-2 and OUJ-2, derived from the DFT calculations at...
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- Published 24 Jul 2019
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Figure 1: Molecular structures of the two target compounds BOD-TTPA-alk and BOD-TTPA, and the chemical struct...
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Figure 2: a) Geometrical optimization of four representative BODIPY-based materials for DSSCs application. b)...
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Figure 3: Predicted absorption spectra of the four dyes.
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Figure 4: Synthetic scheme of the selected materials. a) hydroxylamine hydrochloride, NaHCO3, DMSO, 60 °C the...
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Figure 5: a) Absorption spectra of compounds BOD-TTPA-alk and BOD-TTPA (THF, ≈10−6 M, 25 °C). b) Absorbance s...
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Figure 6: J(V) curves of the best performing DSSCs devices sensitized with compounds BOD-TTPA-alk (blue trace...
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Figure 7: Photovoltaic parameters evolution with the increasing concentration of tBP in the electrolyte.
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- Published 25 Jul 2019
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Figure 1: Aurone ring system and numbering.
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Figure 2: Aurone syntheses.
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Figure 3: UV–vis spectral comparisons in acetonitrile.
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Figure 4: Fabric dying and photobleaching. The top two sets show dyed fabric strips with premordant, simultan...
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- Published 06 Aug 2019
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Figure 1: Some di- and mono-styryl dyes previously reported as fluorescent “light-up” probes for G4-DNA and R...
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Figure 2: Design of a library of di- and mono-styryl dyes. Counter-ions are omitted for the sake of clarity.
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Scheme 1: A, B) General synthesis of A) distyryl and B) mono-styryl dyes via Knoevenagel condensation route. ...
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Scheme 2: Synthesis of I3–5 and I15.
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Figure 3: Representative absorption spectra of distyryl dyes: A) 1d, B) 1ð, C) 1f, D) 1u, E) 10a and F) 12a i...
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Figure 4: Representative absorption spectra of the distyryl dyes (c = 10 µM in MeOH) demonstrating the influe...
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Figure 5: Heat map of the relative emission intensity enhancement (I/I0) of styryl dyes and thioflavin T (ThT...
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Figure 6: Analysis of the light-up response matrix of the dyes. The average light-up factor of each dye with ...
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Figure 7: PC1 vs PC2 plot obtained from the principal component analysis of the light-up data matrix for all ...
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Figure 8: Dual-dye conformational analysis of an extended panel of 33 DNA oligonucleotides. This is performed...
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Figure 9: Selected probes featuring high fluorimetric response towards G4 structures.
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Figure 10: Photographs of solutions of A) distyryl dyes 1p and 1u; B) mono-styryl dyes 17a and 18a, in the abs...
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- Published 08 Aug 2019
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Scheme 1: Conceptual idea for tautomeric metal sensing.
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Scheme 2: 4-(Phenyldiazenyl)naphthalen-1-ol (1) and tautomeric ligands based on it.
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Figure 1: The most stable tautomeric form of 6 in neutral state (left) and upon complexation with Mg(ClO4)2 (...
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Figure 2: Absorption spectra of compounds 1 (a) and 6 (b) in acetonitrile (—), chloroform (− · −), dichlorome...
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Figure 3: Left: Theoretically predicted structure of 6K (blue), overlaid with the X-ray structure (red). Righ...
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Figure 4: Left: Absorption spectra of 6 with stepwise addition of Mg(ClO4)2 in acetonitrile (1 – neutral liga...
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Figure 5: Normalized spectra of the free ligand 6 (c = 5 × 10−5 M) and its complexes obtained with Ba(ClO4)2,...
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Scheme 3: Synthetic route of 6.
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- Published 27 Aug 2019
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Scheme 1: Synthesis of reference NDI 1 and cNDIs 2–6; bottom: image of saturated solutions of cNDIs 2–6 in DM...
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Figure 1: Optical properties of NDI 1 and cNDIs 2 and 6: UV–vis absorbance in CH2Cl2 and in DMF (normal lines...
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Scheme 2: Photocatalytic α-alkylation of octanal (12): 500 mM 12, 250 mM 13, 50 mM (20 mol %) organocatalyst ...
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Figure 2: Normalized absorbance of cNDI 6 in comparison to normalized emission of the 468 nm, 520 nm, 597 nm,...
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Figure 3: Kinetic analysis of yields of product 14 in the presence (solid lines) and in the absence (dashed l...
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- Published 09 Sep 2019
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Figure 1: Structures of some representative triangulenium dyes. a) Rhodamine/fluorescine-like derivatives wit...
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Figure 2: Examples of various types of SNAr reactions typical in triangulenium synthesis, exemplified with th...
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Scheme 1: Synthesis of three novel SX-(DMP)3C+ PF6− ethylsulfanyl-substituted triarylmethylium salts.
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Scheme 2: Synthetic route for the synthesis of S3-ADOTA+.
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Scheme 3: Synthesis of S3-TOTA+ PF6− (6) and the mono ring closed xanthenium 7.
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Scheme 4: Synthesis of S2-TOTA+ PF6− (8) and S1-TOTA+ PF6− (9).
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Figure 3: UV–vis spectra in MeCN: S3-(DMP)3C+ (1, red), S2-(DMP)3C+ (2, green), and S1-(DMP)3C+ (3, blue).
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Figure 4: UV–vis spectra in MeCN: S3-acridinium (4a, black) and S3-xanthenium (7, red). Inset: The 3D structu...
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Figure 5: UV–vis spectra in CH2Cl2: S1-TOTA+ (9, blue line), S2-TOTA+ (8, red line), and S3-TOTA+ (6, black l...
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Figure 6: UV–vis absorption and fluorescence spectra (λex = 485 nm) of 5a in CH2Cl2 solution. Calculated mole...
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Figure 7: Normalized absorption and fluorescence spectra of 6 (S3-TOTA+), λex = 460 nm, and 8 (S2-TOTA+), λex...
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- Review
- Published 24 Sep 2019
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Figure 1: Jablonski-type diagram displaying the classical one-photon excited fluorescence (left), and the les...
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Figure 2: Two ways to represent schematized structures of dendrimers, showing the different generations (laye...
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Scheme 1: Synthesis of phosphorhydrazone dendrimers, from the core to generation 2. Generation 1 dendrimers w...
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Scheme 2: Full structure of the generation 1 dendrimer bearing 12 blue-emitting TPA fluorophores on the surfa...
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Figure 3: Linear structure of the generation 2 dendrimer bearing 24 green-emitting TPA fluorophores on the su...
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Scheme 3: Synthesis of the dioxaborine-functionalized dendrimer of generation 4.
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Figure 4: Diverse structures of multistilbazole compounds, and graph of the σ2max/εmax response, depending on...
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Figure 5: Nile Red derivatives: monomer (M) and two generations of dendrimers.
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Scheme 4: Dumbbell-like dendrimers (third generation) having one TPA fluorophore at the core, and ammonium te...
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Scheme 5: Another example of dumbbell-like dendrimers having one TPA fluorophore at the core, and P(S)Cl2 or ...
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Scheme 6: The 12 steps needed to synthesize a sophisticated TPA fluorophore, to be used as branches of dendri...
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Scheme 7: Synthesis of dendrimers having TPA fluorophores as branches and water-solubilizing functions on the...
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Figure 6: Other types of dendrimers having TPA fluorophores as branches and water-solubilizing functions on t...
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Figure 7: Generations 0, 1, and 2 of dumbbell-like dendrimers having one fluorophore at the core and either 1...
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Figure 8: Double layer fluorescent dendrimer.
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Figure 9: Dumbbell-like dendrimer used for two-photon imaging of the blood vessels of a living rat olfactory ...
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Figure 10: Fluorescent gold complex having high antiproliferative activities against different tumor cell line...
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Figure 11: A fluorescent water-soluble dendrimer, applicable for two-photon photodynamic therapy and imaging.
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Figure 12: Schematization of the different types of TPA fluorescent phosphorus dendrimers and dendritic struct...
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- Full Research Paper
- Published 01 Oct 2019
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Scheme 1: Comparison of optical properties of different silicon rhodamines.
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Scheme 2: Retrosynthetic analysis of the proposed small molecule bimodal probe [18F]16 for both optical and P...
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Scheme 3: Optimization of the HD rearrangement of 19 and subsequent reaction with xanthone 17 to the silicon ...
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Figure 1: (a) Absorption and fluorescence emission spectra of dye 15 measured in PBS buffer pH 7.4. (b, c) Co...
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Figure 2: STED and confocal images of the mitochondrial network in living HeLa cells stained with 1 µM SiR dy...
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Figure 3: Exemplary holographic image sequence of two cell divisions of U2OS cells treated with 1 µM of dye 15...
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- Published 01 Oct 2019
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Figure 1: Structures of “thiophenylated” DAEs prepared and studied in this work.
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Scheme 1: Synthesis routes towards mono- and diiodinated core structures 4, 5, 7, and 8.
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Scheme 2: Synthesis of thiophene- and bithiopheneboronic esters 9 and 12 (bpy – 4,4’-di-tert-butyl-2,2’-dipyr...
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Scheme 3: Photoswitchable diarylethenes AsTh1, SyTh1, AsTh2, SyTh2, AsOTh1, SyOTh1, AsOTh2, and SyOTh2 synthe...
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Scheme 4: Saponification of methyl ester groups in tetraester SyTh2 leading to tetracarboxylic acid SyTh2-H.
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Figure 2: Absorption (A) and emission (B) spectra of SyTh2 in acetonitrile in the course of the cyclization r...
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Figure 3: Absorption spectra of the OFs (A) and CFs (B) of AsTh1 (a), SyTh1 (b), AsTh2 (c), SyTh2 (d), AsOTh1...
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Figure 4: Solutions of compounds AsTh1 (a), SyTh1 (b), AsTh2 (c), SyTh2 (d), AsOTh1 (e), SyOTh1 (f), AsOTh2 (...
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Figure 5: Fatigue resistances of compounds SyOTh1 (A and B) and SyTh1 (C). Parts A and C show the absorbance ...
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Figure 6: (A) Absorption spectra of compound SyOTh1 in MeCN at the photostationary states under irradiation w...
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- Published 25 Oct 2019
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Figure 1: Molecular structure of Nile red (NR).
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Figure 2: Fluorescence (a) and absorption (b) spectra of NR in solvents of different polarity at 25 °C. The s...
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Figure 3: Solvatochromic plot of the absorption (νa) and fluorescence (νf) maxima of NR in a series of solven...
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Figure 4: Absorption (a) and fluorescence (a, b) spectra of NR in PMMA (350 kg/mol) film 500 nm thin at diffe...
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Figure 5: Dependence of the fluorescence maximum (νf) of NR on the excitation wavelength (λe) in rigid PMMA m...
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Figure 6: Absorption (a) and fluorescence (a, b) spectra of NR in ethyl acetate (EtOAc) at different excitati...
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- Published 29 Oct 2019
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Scheme 1: Different synthetic approaches to silicon rhodamine dyes.
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Scheme 2: Previous work from Calitree [29] and Urano [22,28] on the Suzuki–Miyaura coupling of triflates, derived from x...
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Scheme 3: Optimization of cross-coupling conditions of triflate 21, derived from Si-xanthone 12, with boron s...
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Scheme 4: Coupling reactions of silicon xanthone 12 with different boron species (23b–30b, 31).
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- Published 04 Nov 2019
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Figure 1: Structures of the dyes 16–19.
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Scheme 1: Synthesis of the precursors 2, 3, and 5.
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Scheme 2: Synthesis of the precursor triflates 8–11.
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Scheme 3: Synthesis of 12–15 and the organoboron dyes 16–19.
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Figure 2: UV–vis absorption (solid line) and fluorescence (dashed line) spectra of a) 16, b) 17, c) 18, and d...
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Scheme 4: Jablonski diagram representing the photophysical processes in the dyes 16–19.
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Figure 3: Transient absorption spectrum (600 ns delay) of dye 17 in nitrogen-purged acetonitrile on excitatio...
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Figure 4: Fluorescence titrations of the dyes (ca. 4–11 μM) with Bu4NF in acetonitrile. a) 16 (up to 156 equi...
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- Letter
- Published 06 Nov 2019
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Figure 1: The 2,1,3-benzothiadiazole (BTD) core and its derivatives that are successfully applied in bioimagi...
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Scheme 1: Synthesis of the plasma membrane BTD probe (BTD-4APTEG) and its structural features.
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Figure 2: (Left) UV–vis, (center) fluorescence emission and (right) solvatochromic effect (Stokes shift in wa...
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Figure 3: Mean absolute error (MAE) comparing both the experimental and the estimated TD-DFT λmax positions i...
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Figure 4: (A) CAM-B3LYP/6-311+G(d) optimized geometry of BTD-4APTEG (implicit DMSO). (B) TD-DFT UV–vis spectr...
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Figure 5: Cellular viability determined by MTT analysis after 24 h treatment with the developed dye BTD-4APTE...
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Figure 6: MCF-7 cells incubated with BTD-4APTEG (1 μM) in live (A) and (B) and fixed cells (C) and (D). (A) a...
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Figure 7: Co-staining experiments using the commercially available CellMask (red emission) and BTD-4APTEG (gr...
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- Published 12 Nov 2019
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Scheme 1: Consecutive three-component alkynylation–Michael addition–cyclocondensation (AMAC) synthesis of α-p...
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Scheme 2: Consecutive pseudo-four-component alkynylation–Michael addition–cyclocondensation (AMAC) synthesis ...
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Scheme 3: Consecutive pseudo-four-component alkynylation–Michael addition–cyclocondensation (AMAC) synthesis ...
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Scheme 4: Model system for the optimization of the Michael addition–cyclocondensation reaction step to 1H-pyr...
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Scheme 5: Formation of α-pyrone 6a and 1H-pyridine 5a at 20 °C.
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Scheme 6: Formation of α-pyrone 6a starting from alkynone 3b having an electron-donating substituent.
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Scheme 7: Formation of 1H-pyridine 5b starting from alkynone 3d having an electron-withdrawing substituent.
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Scheme 8: Formation of 1H-pyridine 8a by Michael addition–cyclocondensation reaction.
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Scheme 9: Mechanistic rationale for the formation of the 1H-pyridine 5a.
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Scheme 10: Formation of 1H-pyridine 8a from alkynone 3b and dimer 7.
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Figure 1: Molecular structure of 1H-pyridine 5a (50% thermal ellipsoids), showing the intramolecular N–H···O ...
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Figure 2: Supramolecular C–H···N [36-39] and C–H···π [40-49] interactions around the 6-positioned phenyl ring in 5a. Detail...
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Figure 3: 1H-Pyridine derivatives 5 as solids under daylight (top), under UV light (λexc = 365 nm, c(5) = 10−4...
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Figure 4: Selected normalized absorption (solid lines) and emission (dashed lines) spectra of 1H-pyridines 5a...
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Figure 5: Selected normalized emission spectra of 1H-pyridine 5a and 5b in the solid state at T = 298 K.
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Figure 6: Selected normalized absorption (solid lines) and emission (dashed lines) spectra of 1H-pyridines 8a...
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Figure 7: Solid-state luminescence of 1H-pyridines 5a, 8a and 8b (λexc = 365 nm).
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Figure 8: α-Pyrones 6 as solids under daylight (top), selected derivatives under UV light (λexc = 365 nm, c(6...
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Figure 9: Selected normalized absorption spectra of α-pyrones 6a, 6b, 6d, and 6e recorded in dichloromethane ...
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Figure 10: Selected normalized absorption (solid lines) and emission (dashed lines) spectra of α-pyrones 6c, 6e...
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Figure 11: Absorption (top) and fluorescence (bottom) of compound 6c with variable solvent polarity (left to t...
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Figure 12: Absorption (solid lines) and emission (dashed lines) spectra of α-pyrone 6c in five solvents of dif...
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Figure 13: Lippert plot for α-pyrone 6c (n = x, r2 = 0.970).
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Figure 14: Normalized emission spectra of selected α-pyrones 6a–d,f in the solid state at T = 298 K.
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Figure 15: Fluorescence of compound 6e in different THF/water fractions (top, λexc = 365 nm, handheld UV lamp)...
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Figure 16: Selected DFT-computed (B3LYP 6-311G**) Kohn–Sham FMOs for 1H-pyridines 5f and 5g representing contr...
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Figure 17: Selected DFT-computed (B3LYP 6-311G**) Kohn–Sham FMOs for 1H-pyridines 6a, 6c, 6e, 6f, and 6g and r...
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