Open Access Article
Vladyslav Polishchuk
*,
Svitlana Shishkina and
Mykola Shandura
Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Akademika Kukharya Street 5, Kyiv 02094, Ukraine. E-mail: vlad3ds@gmail.com
First published on 27th May 2026
Polymethine dyes incorporating multiple meso-cyano-2,2-difluoro-1,3,2-dioxaborine units as integral components of the π-chain and 1,3,3-trimethyl-2H-indole moieties as donor end-groups were synthesized and characterized. The obtained dyes exhibit an unusual electronic structure that combines merocyanine-like (D–π–A) and polyanionic ([A–π–A′]n) π-conjugated systems within a single mero-polyanionic chromophore, realized in both symmetric (D–π–A–π[–A–π]n–D) and unsymmetric (D–π[–A–π]m–A) architectures. The molecular structures of representative monoanionic dyes from both series were elucidated by X-ray analysis, suggesting a non-uniform distribution of the electron density along the π-conjugated system. These dyes exhibit NIR absorption extending up to 940 nm, with remarkably high molar absorption coefficients of up to 468
000 M−1 cm−1 in DMF. The position of the long-wavelength absorption maximum shows only weak solvent dependence. The shortest-wavelength oligomers of the studied dyes are strongly fluorescent compounds, with quantum yields of 0.10–0.16 for emission around at 800 nm, and display photostability comparable to that of classical cyanine dyes such as indotricarbocyanine iodide (HITC) and indocyanine green (ICG).
Polymethine dyes, such as cyanines and merocyanines, stand out among known classes of organic dyes as intensely absorbing (molar absorption coefficients often exceed 200
000 M−1 cm−1) and strongly fluorescent compounds.29–31 Within the broad structural landscape of polymethines, cyanine dyes featuring pentamethine and heptamethine scaffolds arguably hold the greatest promise for potential applications.32,33 For example, the FDA-approved indocyanine green (ICG) is already widely used for fluorescence-guided surgery and perfusion imaging,34 which prompted extensive research on the development of ICG-like contrast agents with improved characteristics.35 Moreover, cyanines are broadly investigated for applications in advanced bioimaging techniques (e.g., dual-mode,36–38 two-photon imaging37,39), PDT,40,41 PTT,42 and photovoltaics.43,44
The attractiveness of cyanines stems from its high structural tunability, allowing broad range of adjustment of physico-chemical properties.45 A classical design strategy for longer-wavelength cyanines involves extending the π-conjugation, resulting in a ∼100 nm red shift of the absorption and emission maxima per vinylene unit. However, extension of the π-conjugated chain increases susceptibility to excited-state cis–trans isomerization, which becomes the dominant nonradiative deactivation pathway and drastically reduces the fluorescence quantum yield.46 To mitigate excited-state photoisomerization and suppress the nonradiative excited-state decay, an effective strategy is to rigidify the chromophore by bridging the π-conjugated chain.47,48
Bridging of the π-chain of the polymethine dyes can be achieved by introducing the 2,2-difluoro-1,3,2-dioxaborine ring (dioxaborine) into polymethine chain.49 The dioxaborine is a relatively strong electron-accepting group and its introduction into a cyanine platform alters the overall electronic structure of the chromophore from the classical positively charged D–π–D type to a merocyanine-like D–π–A–π–D type (Fig. 1).50 Remarkably, bridging of the indotricarbocyanine π-chain by the dioxaborine is accompanied by a noticeable increase in fluorescence quantum yields (FQY; from Φf = 0.19 for HITC to Φf = 0.72 for 2 in dichloromethane (DCM)).50,51 The dioxaborine-containing polymethines of the D–π–A–π–D and D–π–A types have already been recognized as promising photosensitizers for PDT52 and fluorogenic probes for biomedical research,53 especially in the therapy of Alzheimer's disease.54–56 Accordingly, fusion of the cyanine platform with dioxaborine rings holds great promise as a new strategy toward strongly absorbing and highly fluorescent NIR polymethine dyes.
Previously, we have described the synthesis of ‘hybrid’ mero-anionic dyes of the D–π–A–π–A′ type57 and remarkably bright trianionic58 and tetraanionic59 polymethines of the A′–π[–A–π]n–A′ type, which contain the 1,3,2-dioxaborine core(s) as an integral part of the π-chain. Herein we report the synthesis and characterization of the long-wavelength mero-polyanionic dyes of symmetric D–π–A–π[–A–π]n–D and unsymmetric D–π[–A–π]m–A types, comprising several dioxaborine rings within a cyanine platform. Sequential addition of the dioxaborine fragments both red-shifts the absorption and emission maxima (up to 940 nm) and endows the resulting mero-polyanionic chromophores with distinctive spectral properties, such as exceptionally high molar absorption coefficients.
Symmetric polyanionic dyes (B-series) were synthesized in one step starting from compounds 5 and 10 (Scheme 2). For example, reaction of 5 with hemicyanine 9 in acetonitrile in the presence of triethylamine furnished crude B1, which was subsequently purified by pTLC and converted to the tetra-n-butylammonium salt. The extended B-oligomers B2 and B3 were synthesized by coupling intermediate 10 with dyes 1 and 5, respectively. Owing to the substantially diminished reactivity of the methyl group in anionic dye 5 compared to that in merocyanine 1, the reaction between 5 and 10 proceeds more slowly than between 1 and 10, requiring elevated temperatures and an extended reaction time to achieve completion.
Ion exchange between crude trialkylammonium salts of the target dyes and tetra-n-butylammonium iodide serves two main purposes: additional purification and conversion of the dyes into the more stable tetraalkylammonium salts, as polyanionic dyes with tetraalkylammonium counterions have been reported to exhibit higher stability than those containing trialkylammonium counterions.58 Moreover, the tetraalkylammonium salts of the mero-polyanionic dyes gave suitable crystals for the X-ray diffraction analysis.
Given that the local chemical environment of the meso-carbons, fluorines (11B–19F), and protons (CH3) is not significantly affected within the both series of dyes from 1 to 4, their magnetic environment may indeed be slightly altered, as the incorporation of additional dioxaborine units is accompanied by an increase in negative charge within the—albeit more extended—π-conjugated system. Atoms that are spatially adjacent to a negatively charged π-cloud may thus experience stronger shielding in trianionic or tetraanionic chromophore than in monoanionic, reflected in upfield chemical shifts.
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| Fig. 3 Molecular structures and molecular packing of dyes A1 (a, c and e) and B1 (b, d and f) according to the X-ray diffraction data; thermal ellipsoids are shown at 50% probability level. | ||
The crystal structure of dyes A1 and B1 is apparently influenced by electrostatic interaction between the negatively charged chromophores and positively charged bulky counterions. The packing of A1 features a brickwork-like motif of dye anions; the intervening counter-ions preclude the development of extended π–π stacking (Fig. 3c and S5). Proximal chromophores exhibit only minor overlap via the dioxaborine end-groups, which are separated by ca. 4.3 Å. By contrast, in B1, adjacent dye anions form stacked centrosymmetric π–π dimers, enabling maximal stabilizing electrostatic interactions between the alternating positive and negative charges in their chromophores (Fig. 3f and S7). The pronounced π-stacking interactions within the crystal of B1 are manifested by the remarkably tight packing of adjacent chromophores, with an interplanar separation of only ca. 3.1 Å (Fig. 3d).
| Dye | Solvent | λaa [nm] | ε × 10−5 b [M−1 cm−1] | FWHMac [cm−1] | λfd [nm] | Φfe | ΔνSf [cm−1] | ε·Φf × 10−5 g [M−1 cm−1] |
|---|---|---|---|---|---|---|---|---|
| a Long-wavelength absorption maximum.b Molar absorption coefficient.c Full width at half maximum.d Emission maximum.e Fluorescence quantum yield.f Stokes shift.g Fluorescence brightness.h Dyes A2, A3, A4, B2, and B3 are not soluble enough in MeOH to obtain reliable values of molar absorption coefficient. | ||||||||
| A1 | DCM | 655 | 2.15 ± 0.03 | 1105 | 681 | 0.59 ± 0.03 | 580 | 1.27 |
| MeOH | 647 | 2.10 ± 0.03 | 1330 | 683 | 0.060 ± 0.004 | 815 | 0.13 | |
| DMF | 664 | 2.35 ± 0.03 | 1080 | 691 | 0.071 ± 0.004 | 590 | 0.17 | |
| A2 | DCM | 765 | 3.01 ± 0.04 | 910 | 795 | 0.11 ± 0.1 | 490 | 0.33 |
| MeOH | 748 | —h | 1160 | 789 | 0.017 ± 0.002 | 695 | — | |
| DMF | 767 | 3.13 ± 0.04 | 870 | 795 | 0.018 ± 0.002 | 460 | 0.056 | |
| A3 | DCM | 853 | 3.54 ± 0.05 | 1740 | 880 | 0.010 ± 0.001 | 360 | 0.035 |
| MeOH | 829 | —h | 1840 | 863 | <0.01 | 475 | — | |
| DMF | 847 | 3.52 ± 0.05 | 860 | 873 | <0.01 | 350 | — | |
| A4 | DCM | 921 | 3.21 ± 0.04 | 1820 | 952 | <0.01 | 350 | — |
| MeOH | 895 | —h | 2000 | 934 | <0.01 | 470 | — | |
| DMF | 912 | 4.25 ± 0.04 | 800 | 942 | <0.01 | 350 | — | |
| B1 | DCM | 769 | 3.43 ± 0.04 | 970 | 798 | 0.16 ± 0.1 | 470 | 0.55 |
| MeOH | 761 | 3.45 ± 0.04 | 1040 | 806 | 0.043 ± 0.003 | 735 | 0.15 | |
| DMF | 780 | 3.80 ± 0.05 | 850 | 809 | 0.067 ± 0.004 | 460 | 0.25 | |
| B2 | DCM | 854 | 3.24 ± 0.04 | 1780 | 884 | 0.014 ± 0.001 | 400 | 0.045 |
| MeOH | 839 | —h | 1830 | 874 | <0.01 | 480 | — | |
| DMF | 857 | 3.73 ± 0.05 | 860 | 885 | 0.010 ± 0.001 | 370 | 0.037 | |
| B3 | DCM | 924 | 3.91 ± 0.05 | 1690 | 957 | <0.01 | 370 | — |
| MeOH | 902 | —h | 1850 | 940 | <0.01 | 450 | — | |
| DMF | 919 | 4.68 ± 0.06 | 810 | 950 | <0.01 | 355 | — | |
Both the symmetric (B1–B3) and unsymmetric (A1–A4) dyes display only marginal solvatochromism, although several distinct trends are evident. Thus, upon going from polar non-protogenic DMF to polar protogenic methanol, the absorption maximum shifts hypsochromically by 17–19 nm (208–385 cm−1) for all studied dyes. However, when going from DCM to MeOH as the solvent, the hypsochromic shift of λa progressively increases within the both A and B series from A1 (B1) to A4 (B3); for example, it ranges from Δλa = 8 nm (189 cm−1) for A1 to Δλa = 26 nm (315 cm−1) for A4 (Fig. 4a). Also, in the pair of non-protogenic DCM and DMF, the sign of solvatochromism changes with the chromophore lengthening from A1 (B1) to A4 (B3); for example, for A1, the increase of solvent polarity (DCM → DMF) results in a bathochromic shift of the absorption maximum (Δλa = +9 nm), while for A4 the hypsochromic shift is observed for the same solvent pair (Δλa = −9 nm).
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| Fig. 4 (a) Normalized absorption spectra of dyes A1–A4 in DCM (solid lines) and in MeOH (dotted lines). Absorption spectra of dyes A1–A4 (b) and B1–B3 (c) in DMF. | ||
Tetraanionic A4 and trianionic B3 dyes exhibit exceptionally high molar absorption coefficients (ε), reaching the values of 425
000 M−1 cm−1 and 468
000 M−1 cm−1 (in DMF), respectively (Fig. 4b and c). The molar absorptivities of dyes A3, A2, and B2 are also very high, exceeding 300
000 M−1 cm−1 in both DMF and DCM. Within the A series, the molar absorption increases progressively from A1 to A4 in DMF; however, in DCM this trend terminates at A3, as A4 exhibits lower ε than A3 (321
000 vs. 354
000 M−1 cm−1). Non-linear absorption enhancement is also characteristic of the B series in both DMF and DCM, as dianionic dye B2 exhibits slightly lower ε values than the monoanionic B1. The shape of the absorption bands of all studied dyes is typical of cyanine-like polymethines, featuring an intense and narrow long-wavelength band along with a higher-energy (blue-shifted by 1000–1300 cm−1 from the long-wavelength peak) vibronic shoulder of more than twofold lower intensity. In addition, similarly to long-wavelength classical cyanines, progressive lengthening of the π-conjugated system of the studied dyes results in a gradual increase of the vibronic shoulder relative intensity (Fig. 4). The studied dyes show no changes in their absorption spectra over the concentration range of 0.05–5 µM, thus excluding aggregate formation in the selected solvents (DCM, MeOH, DMF; Fig. S10 and S11).
The brightest fluorescence of the studied dyes is observed in DCM, whereas in MeOH and DMF the emission intensity is much lower. For example, the fluorescence quantum yields (FQY, Φf) of the monoanionic dyes A1 and B1 reach 0.59 and 0.16 in DCM, respectively; which are relatively high values as for NIR-emitting dyes of the polymethine family. However, in MeOH and DMF, the FQYs do not exceed 0.1 for both A1 and B1, while for their higher oligomers (A3, A4, B2, and B3) fluorescence is barely detectable in polar media. In general, within both the A and B series, the fluorescence intensity decreases from A1 (B1) to A4 (B3), consistent for long-wavelength polymethines from the energy gap law (enhanced internal conversion)62 and the increasing propensity for excited-state photoisomerization,63 which promotes non-radiative deactivation. The Stokes shifts (ΔνS) of all studied dyes fall in the range of 26–45 nm (350–810 cm−1) and are scarcely influenced by solvent polarity, though they are generally higher in MeOH than in DCM or DMF (Table 1). Note that, while the optical properties of the studied dyes differ only slightly in DCM and DMF, there are more pronounced changes when going to protogenic MeOH: increased hypsochromic shifts and ΔνS values, as well as broader absorption bands. Given the anionic nature of the studied dyes, these effects may be explained by stronger electrophilic solvation of their chromophores by the protogenic solvent.
The relative stabilities of all obtained dyes were evaluated against the classical cyanines HITC and ICG under controlled conditions. Photodegradation was assessed by comparing absorption intensities before and after 30 min irradiation of dye solutions in MeCN with UV light (λex = 300 nm). The results show that in the HITC/ICG pair, the former is more photostable: after 30 min under the experimental conditions, the absorption of HITC decreased by 7%, whereas that of ICG decreased by 43% (Fig. S12). Dyes absorbing in the 650–750 nm region (A1, A2, and B1) exhibit photostability comparable to HITC (λa = 740 nm in MeCN), whereas longer-wavelength dyes A3, A4, B2, and B3, absorbing in the 850–920 nm range, are comparable to ICG (λa = 784 nm in MeCN). As the π-conjugated system is extended by additional dioxaborine units, photostability decreases linearly in both the A and B series (Fig. S13).
The possible mechanism of light-induced photodegradation involves a photooxidation pathway, in which the photoexcited dye interacts with oxygen to generate reactive oxygen species (ROS). Subsequent reactions of the dyes with ROS lead to their degradation, producing byproducts such as 1-alkyl-3,3-trimethylindolin-2-one and derivatives of Fischer's aldehyde.64 When the experiments were performed under oxygen-free conditions (by bubbling argon through the dye solutions for 10 min), photodegradation under 300 nm irradiation was significantly reduced. For example, under these conditions B3 degraded by only 11% (vs. 59% in non-degassed MeCN), while A4 degraded by 7% (vs. 43% in non-degassed MeCN; Fig. S14). These results indicate that the primary bleaching pathway of the mero-polyanionic dyes is oxygen-dependent, which consistent with the typical degradation behaviour of cyanine dyes.
000 M−1 cm−1 in DCM and 468
000 M−1 cm−1 in DMF. Fluorescence quantum yields are highest for the mono- and dianionic oligomers (0.11–0.59 in DCM), whereas in DMF and MeOH all dyes are weakly fluorescent. The dyes display negligible solvatochromism, minimal fluorochromic behaviour, and small Stokes shifts. As the absorption shifts to longer-wavelengths, photostability decreases linearly in both series, although it remains comparable to that of classical cyanines (HITC and ICG) operating in the same spectral region.
Single crystals of dyes A1 and B1 suitable for X-ray diffraction analysis were obtained by slow evaporation from EtOAc/acetone (1
:
1) solutions. Detailed crystallographic data are provided in the SI. Supplementary crystallographic data for this paper are available under deposition numbers 2548387 (compound A1) and 2548388 (compound B1). These data can be obtained free of charge from the joint Cambridge Crystallographic Data Centre and Fachinformationszentrum Karlsruhe Access Structures service.
The UV-vis-NIR absorption and fluorescence spectra were measured using a Shimadzu UV-3100 spectrophotometer and a Solar CM-2203 spectrofluorometer (modified with a Hamamatsu-S7031 CCD detector for NIR measurements up to 1030 nm), respectively. To minimize the inner filter effects, the optical densities of dye solutions in fluorescence measurements did not exceed 0.1 in the absorption maximum. The fluorescence quantum yields (Φf) were determined relative to ICG (ΦR = 0.13, EtOH) and HIDC (ΦR = 0.28, EtOH).60 The values of Φf were corrected taking into account refractive indexes of the solvents: Φf = ΦR × (I/IR) × (AR/A) × (n2/nR2), where ΦR is the fluorescence quantum yield of the reference dye; I and IR are the integrated fluorescence intensities of the tested compound and the reference dye, respectively; A and AR are the optical densities at the excitation wavelength; n and nR are the refractive indices of the solvents used.
The molar absorption coefficients (ε) were determined according to the Beer–Lambert law by measuring the absorbance of a concentration series for each dye. Solutions were prepared by dissolving precisely weighed amounts of each compound and subsequently diluted to a working concentration range of 0.5–4.0 µM. To ensure the highest accuracy and to exclude the influence of molecular aggregation, the linearity of the absorbance at λa versus concentration was verified through linear regression analysis. All dyes exhibited a linear correlation, confirming the absence aggregation, scattering, or detector saturation effects within the studied range. Data were collected from four independent measurements using 10 mm quartz cuvettes at 25 °C.
Photostability of dyes A1–A4, B1–B3, HITC, and ICG was studied under controlled conditions: dye solutions in acetonitrile with optical densities 0.05–0.10 in the absorption maximum were placed in a 1 cm quartz cuvette in the fluorescent spectrometer (Solar CM2203, 250 W xenon lamp as the excitation source). Photodecomposition of the samples was monitored in “kinetics” mode under continuous irradiation for 30 min at 300 nm, by recording the decrease in fluorescence intensity over time. Slit widths of the excitation monochromator were set to the value of 6 mm, which corresponds to 28.5 nm of excitation bandwidth at half maximum. Photostability was also evaluated by comparing the initial and final absorption spectra of the studied solutions. The 300 nm excitation wavelength was chosen for intrinsic photostability assessment between A1–A4, B1–B3, HITC, and ICG. Under irradiation by 650 nm for 2 h no detectable photodegradation was observed.
CCDC 2548387 and 2548388 contain the supplementary crystallographic data for this paper.65a,b
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