Merocyanines: Synthesis and Application

Merocyanines: Electronic Structure and Spectroscopy in Solutions, Solid State, and Gas Phase

Merocyanines, owing to their readily tunable electronic structure, are arguably the most versatile functional dyes, with ample opportunities for tailored design via variations of both the donor/acceptor (D/A) end groups and π-conjugated polymethine chain. A plethora of spectral properties, such as strong solvatochromism, high polarizability and hyperpolarizabilities, and sensitizing capacity, motivates extensive studies for their applications in light-converting materials for optoelectronics, nonlinear optics, optical storage, fluorescent probes, etc. Evidently, an understanding of the intrinsic structure-property relationships is a prerequisite for the successful design of functional dyes. For merocyanines, these regularities have been explored for over 70 years, but only in the past three decades have these studies expanded beyond the theory of their color and solvatochromism toward their electronic structure in the ground and excited states. This Review outlines the fundamental principles, essential for comprehension of the variable nature of merocyanines, with the main emphasis on understanding the impact of internal (chemical structure) and external (intermolecular interactions) factors on the electronic symmetry of the D-π-A chromophore. The research on the structure and properties of merocyanines in different media is reviewed in the context of interplay of the three virtual states: nonpolar polyene, ideal polymethine, and zwitterionic polyene.

Design and Photonics of Merocyanine Dyes

Merocyanines, thanks to their easily adjustable electronic structure, appear to be the most versatile and promising functional dyes. Their D-π-A framework offers ample opportunities for custom design through variations in both donor/acceptor end-groups and the π-conjugated polymethine chain, and leads to a broad range of practical properties, including noticeable solvatochromism, high polarizability/hyperpolarizabilities, and the ability to sensitize various physicochemical processes. Accordingly, merocyanines are applied and extensively studied in various fields, such as light-converting materials for optoelectronics, nonlinear optics, optical storage, solar cells, fluorescent probes, and antitumor agents in photodynamic therapy. This review encompasses both classical and novel more important publications on the structure-property relationships in merocyanines, with particular emphasis on the results by A.  I. Kiprianov and his followers in Institute of Organic Chemistry in Kyiv, Ukraine.

Cyclohexene-Embedded Dicyanomethylene Merocyanines - Consecutive Three-Component Coupling-Addition Synthesis and Chromophore Characteristics

A concise and efficient consecutive three-component alkynylation-addition synthesis of cyclohexene-embedded dicyanomethylene merocyanines furnishes a small library of dyes in moderate to excellent yield. The dyes possess strong absorption coefficients of the longest wavelength absorption bands. According to the crystal structure, the small bond length alternations account for a highly delocalized electronic ground state. The electronic structure of the absorption bands is qualitatively rationalized by TDDFT calculations, which explain that intense HOMO-LUMO transitions along the merocyanine axis lead to cyanine similar Stokes shifts.

A novel strategy for the functionalization and design of 4-methylene-4H-pyran merocyanines via enamination and 1,8-conjugate addition

4-Methylene-4H-pyrans are popular merocyanine dyes, but their functionalization is limited by the Knoevenagel condensation with aromatic aldehydes. In this work, we developed a novel approach for the construction of a new class of pyran fluorophores based on enamination and subsequent nucleophilic substitution of the dimethylamino group via 1,8-conjugate addition/elimination. This methodology includes selective transformations leading to previously unknown symmetrical and asymmetrical structures. The dimethylaminovinyl-substituted pyrans are reactive intermediates and can be considered as a convenient synthetic tool for the construction of new merocyanines with tunable fluorescence (417-628 nm). The main strategies for the modification of the pyran moiety have been determined for the construction and targeted design of fluorophores. Pyrans bearing two enamine moieties demonstrate significant light extinction coefficients (up to 116 000 M^-1 cm^-1), high quantum yields (up to 69%) and large Stokes shifts (up to 152 nm) because of their strong push-pull nature. Density Functional Theory (DFT) calculations were performed for the explanation of the structural and photophysical features of the prepared merocyanines. The developed approach can be considered as a useful platform for further application of 4-methylene-4H-pyrans as promising fluorophores for sensors and solar cells, and in bioimaging.

Merging liquid crystalline self-assembly and linear optical properties of merocyanines via tailored donor units

Aiming at merocyanine dyes with good linear optical and self-assembly properties, a series of rigid mono-, bi- and tricyclic merocyanines with O- and N-donor units as well as keto or...

Three-Component Suzuki-Knoevenagel Synthesis of Merocyanine Libraries and Correlation Analyses of Their Oxidation Potentials and Optical Band Gaps

The Suzuki coupling Knoevenagel condensation one-pot synthesis of boronic acids/esters, (hetero)aromatic bromo aldehydes and methylene active compounds is a highly practical consecutive three-component process to provide substance libraries with 60 donor-π-bridge-acceptor molecules, i.e., merocyanines in a broader sense, in moderate to excellent yield. As already seen with the naked eye, a broad variation of the optical properties becomes accessible using this practical synthetic tool. More systematically, correlation analyses upon plotting the optical band gaps against the first oxidation potentials of redox active systems of consanguineous series furnishes linear correlations and, by extension, two parameter plots (oxidation potential and emission maximum) planar correlations with the optical band gaps.

Highly Effective Sensitizers Based on Merocyanine Dyes for Visible Light Initiated Radical Polymerization

The 5-(4-substituted-arylidene)-1,3-dimethylpyrimidine-2,4,6-triones were tested as visible light sensitizers for phenyltrialkylborate salts applied to initiate polymerization processes. The initiation occurs as a result of photoinduced electron transfer from the borate salt to the merocyanine dye. The main factor that facilitates the step of the reaction is the free energy change for electron transfer. Its value is favorable according to the reduction properties of the dyes influenced by the type of amino groups and the oxidation potentials of the borate salts. The observed bleaching of the dyes during photopolymerization affects the yield of both the alkyl radical and sensitizer-based radical formation and thus the efficiency of the photopolymerization.

Membrane-Permeant, Environment-Sensitive Dyes Generate Biosensors within Living Cells

Dyes with environment-sensitive fluorescence have proven useful to study the spatiotemporal dynamics of protein activity in living cells. When attached to proteins, their fluorescence can reflect protein conformational changes, post-translational modifications, or protein interactions. However, the utility of such dye-protein conjugates has been limited because it is difficult to load them into cells. They usually must be introduced using techniques that perturb cell physiology, limit throughput, or generate fluorescent vesicles (e.g., electroporation, microinjection, or membrane transduction peptides). Here we circumvent these problems by modifying a proven, environment-sensitive biosensor fluorophore so that it can pass through cell membranes without staining intracellular compartments and can be attached to proteins within living cells using unnatural amino acid (UAA) mutagenesis. Reactive groups were incorporated for attachment to UAAs or small molecules (mero166, azide; mero167, alkyne; mero76, carboxylic acid). These dyes are bright and fluoresce at long wavelengths (reaching ε = 100 000 M^-1 cm^-1, ϕ = 0.24, with excitation 565 nm and emission 594 nm). The utility of mero166 was demonstrated by in-cell labeling of a UAA to generate a biosensor for the small GTPase Cdc42. In addition, conjugation of mero166 to a small molecule produced a membrane-permeable probe that reported the localization of the DNA methyltransferase G9a in cells. This approach provides a strategy to access biosensors for many targets and to more practically harness the varied environmental sensitivities of synthetic dyes.

Structural Modulation of Chromic Response: Effects of Binding-Site Blocking in a Conjugated Calix[4]pyrrole Chromophore

Herein, we modulate the chromic response of a highly colored tetrapyrrole macrocycle, namely, tetrakis(3,5-di-tert-butyl-4-oxocyclohexadien-2,5-yl)porphyrinogen (OxP) by structural modification. N-Benzylation at the macrocyclic nitrogen atoms leads to stepwise elimination of the two calix[4]pyrrole-type binding sites of OxP and serial variation of the chromic properties of the products, double N-benzylated Bz₂OxP and tetra N-benzylated Bz₄OxP. The halochromic (response to acidity) and solvatochromic (response to solvent polarity) properties were studied by using UV/Vis spectroscopy and NMR spectroscopy in nonpolar organic solvents. Titration experiments were used to generate binding isotherms to elucidate their binding properties with difluoroacetic acid. Differences in the halochromic properties of the compounds allowed construction of a colorimetric scale of acidity in nonpolar solvents, as the compounds in the series OxP, Bz₂OxP, and Bz₄OxP are increasingly difficult to protonate but maintain their propensity to change color upon protonation. The concurrent effects of binding-site blocking and modulation of acidity sensitivity are important new aspects for the development of colorimetric indicators.

Increasing Photovoltaic Performance of an Organic Cationic Chromophore by Anion Exchange

A symmetrical cyanine dye chromophore is modified with different counteranions to study the effect on crystal packing, polarizability, thermal stability, optical properties, light absorbing layer morphology, and organic photovoltaic (OPV) device parameters. Four sulfonate-based anions and the bulky bistriflylimide anion are introduced to the 2-[5-(1,3-dihydro-1,3,3-trimethyl-2H-indol-2-ylidene)-1,3-pentadien-1-yl]-1,3,3-trimethyl-3H-indolium chromophore using an Amberlyst A26 (OH^- form) anion exchanger. Anionic charge distribution clearly correlates with device performance, whereby an average efficiency of 2% was reached in a standard bilayer organic solar. Evidence is given that the negative charge of the anion distributed over a large number of atoms is significantly more important than the size of the organic moieties of the sulfonate charge carrying group. This provides a clear strategy for future design of more efficient cyanine dyes for OPV applications.

Ratiometric Imaging Using a Single Dye Enables Simultaneous Visualization of Rac1 and Cdc42 Activation

Biosensors that report endogenous protein activity in vivo can be based on environment-sensing fluorescent dyes. The dyes can be attached to reagents that bind selectively to a specific conformation of the targeted protein, such that binding leads to a fluorescence change. Dyes that are sufficiently bright for use at low, nonperturbing intracellular concentrations typically undergo changes in intensity rather than the shifts in excitation or emission maxima that would enable precise quantitation through ratiometric imaging. We report here mero199, an environment-sensing dye that undergoes a 33 nm solvent-dependent shift in excitation. The dye was used to generate a ratiometric biosensor of Cdc42 (CRIB199) without the need for additional fluorophores. CRIB199 was used in the same cell with a FRET sensor of Rac1 activation to simultaneously observe Cdc42 and Rac1 activity in cellular protrusions, indicating that Rac1 but not Cdc42 activity was reduced during tail retraction, and specific protrusions had reduced Cdc42 activity. A novel program (EdgeProps) used to correlate localized activation with cell edge dynamics indicated that Rac1 was specifically reduced during retraction.

One-pot three-component synthesis and photophysical characteristics of novel triene merocyanines

Novel triene merocyanines, i.e. 1-styryleth-2-enylidene and 4-(1,3,3-trimethylindolin-2-ylidene)but-2-en-1-ylideneindolones are obtained in good to excellent yields in a consecutive three-component insertion Sonogashira coupling-addition sequence. The selectivity of either series is remarkable and has its origin in the stepwise character of the terminal addition step as shown by extensive computations on the DFT level. All merocyanines display intense absorption bands in solution and the film spectra indicate J-aggregation. While 1-styryleth-2-enylideneindolones show an intense deep red emission in films, 4-(1,3,3-trimethylindolin-2-ylidene)but-2-en-1-ylideneindolones are essentially nonemissive in films or in the solid state. TD-DFT computations rationalize the charge-transfer nature of the characteristic broad long-wavelength absorptions bands.

Environment-sensing merocyanine dyes for live cell imaging applications

Fluorescent biosensors based on environmentally sensitive dyes enable visualization and quantification of endogenous protein activation within living cells. Merocyanine dyes are especially useful for live cell imaging applications, as they are extraordinarily bright, have long wavelengths of excitation and emission, and can exhibit readily detectable fluorescence changes in response to environment. We sought to systematically examine the effects of structural features on key photophysical properties, including dye brightness, environmental responsiveness, and photostability, through the synthesis of a library of 25 merocyanine dyes, derived from combinatorial reaction of 5 donor and 5 acceptor heterocycles. Four of these dyes showed optimal properties for specific imaging applications and were subsequently prepared with reactive side chains and enhanced aqueous solubility using a one-pot synthetic method. The new dyes were then applied within a biosensor design for Cdc42 activation, where dye mero60 showed a remarkable 1470% increase in fluorescence intensity on binding activated Cdc42 in vitro. The dye-based biosensors were used to report activation of endogenous Cdc42 in living cells.

Octupolar merocyanine dyes: a new class of nonlinear optical chromophores

A set of new octupolar merocyanine chromophores was designed and synthesized. These compounds were prepared from the reaction of 1,3,5-triformyl-2,4,6-trihydroxybenzene with heterocyclic nucleophiles. Octupolar dyes were formed exclusively in their open-dye form. The one- and two-photon-absorption spectra of the dyes consist of two bands: The long-wavelength band in the two-photon absorption spectrum (a few hundreds GM above 1000 nm) matches well with the intense, long-wavelength-absorption band that is located in the visible region in the linear spectrum. Interestingly, an additional, much-more-intense TPA band in the NIR region is observed at higher energy, which corresponds to a weakly allowed one-photon electronic transition. Changing the peripheral heterocyclic moieties allows tuning of the optical properties to approach the cyanine limit (i.e., polymethine state), thus resulting in a red-shift of the low-energy one-photon-absorption band as well as to the rise of an intense two-photon-absorption band in the NIR region. To the best of our knowledge, this is the first synthesis and TPA characterization of octupolar merocyanine chromophores with typical low-bond-length alternation.

Self-deprotonation and colorization of 1,3-bis(dicyanomethylidene)indan in polar media: a facile route to a minimal polymethine dye for NIR fluorescence imaging

Colorless 1,3-bis(dicyanomethylidene)indan is an organic acid (pK(a) ≈3.0) that turns blue in polar media owing to self-deprotonation. Moreover, its colored conjugate base shows potential as a minimal anionic polymethine dye for probing biomolecules in cells and in vivo through noncovalent complexation and near-infrared fluorescence signaling.

Spin-carrying benzoquinone derivatives

Several 1,4-benzoquinone derivatives carrying oxy-TEMPO radical(s) at the 2-position or 2,5-positions were found to give black crystals by recrystallization from pale yellow solutions and it was revealed from their crystal structures that unusual single-component CT complexes were formed, in which a nitroxide moiety plays the roll of a donor part and a 1,4-benzoquinone group of the same molecule works as an acceptor part, respectively. On the contrary, no CT formation was found for the derivatives carrying oxy-TEMPO radicals at 2,6-positions and one of the TEMPO groups contributes to a CT formation in a 1,4-benzoquinone derivative carrying amino-TEMPO radicals at 2,5-positions derived from fluoranil, while the other one has a close oxygen-to-oxygen contact with another neighboring molecule to give a very large exchange coupling of J/k(B) = -154 K.

Synthesis of unsymmetric cyanine dye via merocyanine and their interaction with DNA

An effective method has been developed for synthesis of neutral merocyanine dye 4 from (4-nitrophenyl)malondialdehyde. Merocyanine 4 was used as a basic building block for preparation of unsymmetric cyanine dyes 9 and 10, both derived from the same aromatic malondialdehyde. With the cyanine 10, pH-dependent affinity to DNA has been studied. Unsymmetric cyanine dye 10 has been compared with symmetric dye 8. The corresponding binding constants (K) have been calculated for various pH.