Asymmetric Dyes Research Articles

Synthesis, properties and bioconjugation of water-soluble asymmetric indodicarbocyanine dyes

New indodicarbocyanine dyes have been synthesised and converted into succinimidyl active esters for the fluorescent labeling of proteins and oligonucleotides.

Novel asymmetric indodicarbocyanine dyes

Novel indodicarbocyanine dyes functionalized at position 5 of the indolenine system were obtained and characterized by spectroscopic methods.

One‐Pot Synthesis of New Symmetric and Asymmetric Xanthene Dyes.

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One-pot synthesis of new symmetric and asymmetric xanthene dyes

Symmetric and asymmetric xanthene dyes have been prepared by a convenient one-step procedure from aldehyde and diol or m-aminophenol precursors using concentrated phosphoric acid as a solvent. This protocol provides access to water-soluble dyes with large Stoke’s shifts and far-red fluorescence emission. These compounds are envisioned as components of fluorescence-based sensors for a variety of imaging applications.

Novel symmetrical and asymmetrical disaryl hydrazono sulphur-containing direct dyes as possible alternatives for benzidine-based dyestuffs

Two novel series of disaryl azo 2-(thiadiazin-2-yl)-1,2,4-benzothiadiazine-based direct dyes have been synthesized. The produced dyes, being accommodating solubilizing functions, are likely to undergo oxidation and/or hydrolysis to soluble metabolites thus ensure lack of carcinogenicity and in turn, might satisfy the basic requirements for a satisfactory replacement of the prohibited benzidine-based dyes. The assigned structures for the hitherto prepared dyes were confirmed on the basis of elemental analysis and spectral data and, whenever possible, by alternative synthetic routes. Moreover, the predominant tautomeric forms for these highly colored dyes were tested and discussed on the basis of different spectral investigations.

Protein labeling with red squarylium dyes for analysis by capillary electrophoresis with laser-induced fluorescence detection

Two new red luminescent asymmetric squarylium dyes (designated "Red-1c and Red-3") have been shown to exhibit absorbance shifts to longer wavelengths upon the addition of protein, along with a concomitant increase in fluorescence emission. Specifically, the absorbance maxima for Red-1c and Red-3 dyes are 607 and 622 nm, respectively, in the absence of HSA, and 642 and 640 nm in the presence of HSA, making the excitation of their protein complexes feasible with inexpensive and robust diode lasers. Fluorescence emission maxima, in the presence of HSA, are 656 and 644 nm for Red-1c and Red-3, respectively. Because of the inherently low fluorescence of the dyes in their free state, Red-1c and Red-3 were used as on-column labels (that is, with the dye incorporated into the separation buffer), thus eliminating the need for sample derivatization prior to injection and separation. A comparison of precolumn and on-column labeling of proteins with these squarylium dyes revealed higher efficiencies and greater sensitivities for on-column labeling, which, when conducted with a basic, high-salt content buffer, permitted baseline resolution of a mixture of five model proteins. LOD for model proteins, such as transferrin, alpha-lactalbumin, BSA, and beta-lactoglobulin A and B, labeled with these dyes and analyzed by CE with LIF detection (CE-LIF) were found to be dependent upon dye concentration and solution pH, and are as low as 5 nM for BSA. Satisfactory linear relationships between peak height (or peak area) and protein concentration were obtained by CE-LIF for this on-column labeling method with Red-3 and Red-1c.

Two-photon anisotropy: Analytical description and molecular modeling for symmetrical and asymmetrical organic dyes

One- and two-photon anisotropy spectra of a series of symmetrical and asymmetrical polymethine (PD) and fluorene molecules were measured experimentally and discussed theoretically within the framework of three-state and four-state models. For all the molecules discussed in this paper, the experimental two-photon anisotropy values, r 2PA, lie in the relatively narrow range from 0.47 to 0.57 and remain almost independent of wavelength over at least two electronic transitions. This is in contrast with their one-photon anisotropy, which shows strong wavelength dependence, typically varying from ≈0 to 0.38 over the same transitions. A detailed analysis of the two-photon absorption (2PA) processes allows us to conclude that a three-state model can explain the 2PA anisotropy spectra of most asymmetrical PDs and fluorenes. However, this model is inadequate for all the symmetrical molecules. Experimental values of r 2PA for symmetrical polymethines and fluorenes can be explained by symmetry breaking leading to the deviation of the orientation of the participating transition dipole moments from their “classical” orientations.

Synthesis and characterisation of monomethine cyanine dyes based on N ‐bridgehead heterocycles

In this paper, the synthesis and spectral properties of novel asymmetrical and symmetrical monomethine cyanine dyes are described. Reaction of phenylpyrazolones and oxazolones with acetyl thiourea and/or thiosemicarbazideafforded acetyl intermediate compounds which were then reacted with metal divalent chlorides, followed by reaction with N-methyl hetetrocyclic quaternary salts, to give asymmetrical monomethine cyanine dyes. Reaction of the 5-amino derivative of the intermediate compounds with acetaldehyde followed by reaction with N-methyl hetetrocyclic quaternary salts produced the symmetrical monomethine cyanine dyes. These new compounds were characterised with elemental analyses, visible absorption and infrared spectrometry, and 1 H/ 1 3 C NMR and mass spectroscopy. The correlation between the colour and structure of these dyes was also investigated.

Effect of the thickness of a dicarbocyanine dye layer on the conformational composition and spatial orientation of layer components

The conformational and aggregate structure and the spatial orientation of polyatomic organic molecules on solid substrates are investigated by the example of molecular layers of symmetric and asymmetric dicarbocyanine dyes. It is shown that the structure of a dicarbocyanine dye layer is determined by two mechanisms: (i) the change in the symmetry of the intramolecular charge distribution in the monomeric components of the layer as a result of the intermolecular interaction with the substrate, which leads to closer values of the equilibrium concentrations of two monomers with different spatial structure (rotational stereoisomers), and (ii) the association of monomer molecules with formation of dimers and J aggregates. The relative position of the spectra of the layer components, the spatial orientation of the components, and the concentration ratio of different monomeric forms depend on the structure and the electron-donating ability of terminal groups. In going from a monomolecular layer to multilayered structures, the asymmetry of the intramolecular charge distribution induced by the substrate and the ratio of different stereoisomeric forms first change and then become stabilized.

Synthesis and spectral properties of polymethine dyes derived from 5-methyl-11-phenyl-5 H-indeno[2,1- b]quinoline

Based on the 5-methyl-11-phenyl-5 H-indeno[2,1- b]quinoline nucleus, symmetric and unsymmetric cationoid polymethine dyes as well as merocyanines have been synthesized, and their absorption spectra have been studied. As shown, the absorption maxima are shifted with reference to the analogous oxa-compounds hypsochromically for symmetric or strongly asymmetric (containing the low-electron-donor second end residue) dyes, and bathochromically for slightly asymmetric (containing the high- or medium-electron-donor second end residue) dyes.

Thiazoline and thiazoloxazole in synthesis of novel meso-substituted mono-, tri-, and hepta-methine cyanine dyes

2-Cyanomethylene (2-ethoxy carbonylmethylene)-4,5-dihydrothiazolin-4-one 1a,b and 2-cyanomethylene (2-ethoxy carbonylmethylene)-4,5-dihydrothiazolo [3,2-a]oxazole 3a, b were synthesized as starting material. Reaction of both compounds 2a, b and 3a, b with N-methylheterocyclic quaternary salts afforded meso-substituted monomethine cyanine dyes 4a– d and 9a– d, respectively. Reaction of compounds 1a, b and 8a, b with ethyl orthoformate gave the intermediate compounds 5a, b and 10a, b, followed by the reaction with 1,2-dimethyl quinolinium iodide resulted in meso-substituted trimethine cyanine dyes 6a, b and 11a, b, respectively. Also, reaction of both 2a, b and 3a, b with 2-chlorocyclohexane-1,3-dicarboxaldehyde followed by the reaction with 1,2-dimethyl quinolinium iodide afforded the asymmetrical heptamethine dyes 8a, b and 13a, b. The new compounds were characterized by elemental analysis, visible absorption, 1H NMR, IR Spectroscopy and Ms spectral data. Relation between the constitution and the UV/Vis spectroscopic properties of these dyes has been studied.

Thermodynamic characterization of the dimerization equilibrium of an asymmetric dye by spectral titration and chemometric analysis

The monomer–dimer equilibrium of an asymmetric cyanine dye has been investigated by means of UV-Vis spectroscopy. The data have been processed by a recently developed chemometric method for quantitative analysis of undefined mixtures, that is based on simultaneous resolution of the overlapping bands in the whole set of absorption. In this work the dimerization constant of 1-carboxydecyl-4-{3-[3-methyl-3H-benzothiazol-2-ylidene]-propenyl}-quinolinium (TO-3) has been determined by studying the dependence of absorption spectrum on temperature in the range 25–72.5 °C at different total concentrations of dye (8.5×10 −6 to 2.87×10 −5 M). Utilizing the van’t Hoff relation, which describes the dependence of the equilibrium constant on temperature, as constraint we determine the spectral responses of the monomer and dimer species as well as the enthalpy and entropy of the dimerization equilibrium.

Symmetric and asymmetric squarylium dyes as noncovalent protein labels: a study by fluorimetry and capillary electrophoresis

Noncovalent interactions between two squarylium dyes and various model proteins have been explored. NN127 and SQ-3 are symmetric and asymmetric squarylium dyes, respectively, the fluorescence emissions of which have been shown to be enhanced upon complexation with proteins such as bovine serum albumin (BSA), human serum albumin (HSA), β-lactoglobulin A, and trypsinogen. Although these dyes are poorly soluble in aqueous solution, they can be dissolved first in methanol followed by dilution with aqueous buffer without precipitation, and are then suitable for use as fluorescent labels in protein determination studies. The nature of interactions between these dyes and proteins was studied using a variety of buffer systems, and it was found that electrostatic interactions are involved but not dominant. Dye/protein stoichiometries in the noncovalent complexes were found to be 1:1 for SQ-3, although various possible stoichiometries were found for NN127 depending upon pH and protein. Association constants on the order of 10 5 and 10 7 were found for noncovalent complexes of SQ-3 and NN127, respectively, with HSA, indicating stronger interactions of the symmetric dye with proteins. Finally, HSA complexes with NN127 were determined by capillary electrophoresis with laser-induced fluorescence detection (CE–LIF). In particular, NN127 shows promise as a reagent capable of fluorescently labeling analyte proteins for analysis by CE–LIF without itself being significantly fluorescent under the aqueous solution conditions studied herein.

Properties and the nature of electric-field-induced variations in optical absorption spectra of polymethine dyes in polymer matrices

The effect of a permanent electric field on the absorption spectra of ionic (cationic and anionic) and intraionic symmetric and asymmetric polymethine dyes in poly-N-epoxypropylcarbazole, polyvinylbutyral, and polystyrene polymer films is studied. It is found that the electric field causes an increase in absorption of symmetric dyes in the short-wavelength region and a decrease in their absorption in the long-wavelength region. Asymmetric dyes exhibit opposite properties. These properties are common for these groups of dyes irrespective of their chemical structure and ionic nature. They are retained both in photoconducting polymers and in polymers that are incapable of charge photogeneration. These effects also take place in liquid solutions, although in this case they are much weaker. Various mechanisms of the influence of an electric field on the spectra, such as the electron transfer, Stark and Kerr effects, intermolecular interactions, and dye isomerization, are discussed. It is shown that the spectral effects are caused by the redistribution of the electron density in a chromophore of the dye in the ground state resulting in a change in the probability of vibronic transitions.

The Molecular Structures and Properties of Anthraquinone-Type Dichroic Dyes

Relations between the molecular structures and properties of anthraquinone-type dichroic dyes were studied. Newly developed asymmetric dyes with thiophenyl groups are highly soluble in fluorinated liquid crystals and the dichroic ratios of these dyes are high (about 10). However, ortho-position (thiophenyl)-substituted dyes have lower solubilities and dichroic ratios than other position-substituted dyes. The properties of anthraquinone dyes with anilino groups are much lower than those of dyes with thiophenyl groups. These results can be strongly related to the flexibility of substituents. We newly established a hypothesis concerning dyes in liquid crystal solvent. In liquid crystals, the dye has a suitable conformation to adjust to liquid crystal phase. In this conformation, the solubilities and dichroic ratios are increased because the interactions between the dye molecules and liquid crystal molecules are strengthened. Flexible substituents are considered to easily form a suitable conformation and realize excellent properties.

Electronically asymmetric triphenylmethane dyes. Half-methoxy analogues of Malachite Green

A series of derivatives of 4-dimethylamino-4′-methoxytriphenylmethanol has been prepared and the electronic absorption spectra and lightfastness properties of the derived cationic dyes determined. The introduction of one terminal methoxy group results in an electronically unsymmetrical system, to which PMO treatment appears inapplicable. The effects of substitution on the values of λ max x and λ max y are accounted for in terms of bond rotation about essential double or single bonds in an unsymmetrical cyanine chromophoric system and by restoration of electronic symmetry.

Synthesis and properties of near-infrared absorbing asymmetric pyrylium–squarylium dyes containing tertiary butyl groups

Asymmetric pyrylium–squarylium dyes ( 5a– b) were prepared by direct condensation of squaric acid with two different kinds of heterocycles. Symmetrical dyes 5d–f were isolated as by-products. Asymmetric dye 5c was synthesized via the traditional way using monosubstituted squaric acid as the key intermediate. Dyes 5a–f were characterized with the aid of 1H-NMR, IR, mass spectroscopy and elemental analysis. The dyes exhibit high melting points and absorption maxima in the range of 720–760 nm with high extinction coefficients and higher solubility in organic solvents than other squarylium dyes.

Ground- and Excited-State Isomerization of Triphenylmethane Dyes in the Femtosecond Regime

We previously confirmed the existence of two ground-state isomers of crystal violet (CV) in alcohol (Maruyama, Y.; Ishikawa, M.; Satozono, H. J. Am. Chem. Soc. 1996, 118, 6257). These isomers are called “solvation isomers” because they are differentiated by the solvation of alcohol. Here, to investigate if solvation isomers are possible in triphenylmethane (TPM) dyes other than CV, we measured transient differential absorption (ΔOD) spectra of two classes of TPM dyes: symmetric (ethyl violet and parafuchsin) and asymmetric (malachite green and brilliant green) using a femtosecond spectral hole-burning technique. The symmetric TPM dyes that we studied (including CV) showed two spectral holes in the early part of photobleaching, whereas the asymmetric dyes showed three spectral holes. The ΔOD spectra of all of the TPM dyes depended on the pump wavelength. This dependence is the key experimental observation that confirms the existence of ground-state isomers, and thus the asymmetric TPM dyes have three ground-state isomers. Solvation isomers are possible in TPM dyes in alcohol. To obtain insight into the deactivation mechanism of TPM dyes, we examined a plateau region that appears in the early part of photobleaching recovery. The plateau is evidence for the existence of an intermediate state between the lowest singlet excited state (S1) and the ground state. The absence of the plateau only in parafuchsin, which is due to the difference in a positive charge distribution on a nitrogen atom, suggests that the intermediate state is a distorted excited state in which a positive charge is partially shifted to a nitrogen atom in an amino group.

Preparation of monomethine cyanine dyes as noncovalent labels for nucleic acids

By condensation of quaternary benzothiazolium, quinolinium and acridinium salts having an active methyl group with 1-(3-bromopropyl)-4-chloroquinolinium or 1-(3-bromo-2-hydroxypropyl)-4-chloroquinolinium salts in the presence of a basic agent such as triethylamine, 8 asymmetric and symmetric monomethine cyanine dyes bearing ω-bromopropyl substituent with one or two positive charges, were synthesized. Additionally, two of the dyes were quaternized with pyridine, and monomethine cyanines with two and three positive charges are prepared. Most of the dyes showed high molar absorptivity (70 000–100 000 l mol −1 cm −1). The acridinium dyes showed broad peaks with lower intensity of 30 000 l mol −1 cm −1. In the presence of nucleic acid in aqueous solutions, a strong enhancement of the fluorescence of these new dyes was observed.

Ion pairs of indobenzimidazolo cyanines: a structural study based on conductivity, absorption, fluorescence and [formula omitted]-NMR

Asymmetric benzimidazolo carbo, di- and tricarbocyanines form ion pairs of the solvent-separated and contact types with different counterions in tetrahydrofuran, toluene and toluene–nitrile mixtures. The dissociation constants of the ion pairs in tetrahydrofuran, evaluated from conductivity data, do not depend on the length of the polymethine chain and show only a small decrease with decreasing counterion size. The absorption and fluorescence excitation spectra of the contact ion pairs exhibit a pronounced hypsochromic shift with respect to the solvated ions and the solvent-separated ion pairs. 1 H−NMR experiments have provided information about the electronic structures of the ions of both the asymmetric dyes and the corresponding symmetric carbocyanines. They have also revealed different preferred anion locations in the contact ion pairs of the symmetric indocarbocyanine on one hand, and of the benzimidazolo carbocyanine and the asymmetric dyes on the other. This structural difference is suggested to be a cause of the observed opposite effects of ion pairing on the isomerization kinetics of the two groups of dyes.