Dye Monomers Research Articles

Synthesis of novel monomeric cyanine dyes containing 2-hydroxypropyl and 3-chloro-2-hydroxypropyl substituents – Noncovalent labels for nucleic acids

Several novel mono-, di- and tricationic monomethine cyanine dyes belonging to the Thiazole Orange family have been prepared via an improved synthetic procedure. The dyes, useful for nucleic acid detection, bear 2-hydroxypropyl and 3-chloro-2-hydroxypropyl substituents. All derivatives absorb in the region 476–519 nm and have a molar absorptivity of 49 000–106 000 L mol −1 cm −1. The reaction products were characterized by 1H NMR spectroscopy and elemental analysis.

Synthesis of novel monomeric and homodimeric cyanine dyes with thioacetyl substituents for nucleic acid detection

Several novel di-, tri- and tetracationic monomeric and homodimeric monomethine cyanine dyes for nucleic acid detection were synthesized by condensation of 3,4-dihydro-(2 H)-1,3-thiazino[2,3- b]benzooxazolium bromide and appropriate 1-( ω-bromoalkyl)-4-methylpyridinium or 1-( ω-bromoalkyl)-4-methylquinolinium bromide followed by quaternization with N, N, N′, N′-tetramethyl-1,3-propanediamine (TMPDA) or N, N, N, N′, N′-pentamethyl-1,3-propanediammonium iodide, or bisquaternization with TMPDA or N, N, N′, N′-tetramethyl-1,6-hexanediamine (TMHDA).

Synthesis, thermal and optical properties of liquid crystalline terpolymers containing azobenzene and dye moieties

The synthesis, thermal properties and photochemical and photophysical studies of new azopolymers are described. These polymers contain three different types of monomer, each of which is mainly responsible for a particular function: A mesogenic benzanilide, a photochromic azobenzene and a dye unit (a benzoxazole, an anthracene or a stilbene derivative). This approach provides liquid crystalline terpolymers with different spectral properties and with the potential ability to be photoaligned by irradiation and thermotropic self-organization. The polymers have been prepared by random radical polymerisation of the corresponding methacrylate-fucntionalised units. All of the materials show good thermal stability and liquid crystalline behaviour, displaying smectic A or nematic mesophases. Optical properties of the polymers in solution display additive bands in the absorbance spectrum and luminescent properties in the emission region of the individual dye monomers. However, films of these polymers are not luminescent. A study of the absorption and redox properties of the dyes has been performed in order to evaluate the quenching process in the polymers.

Synthesis of novel monomeric cyanine dyes containing mercapto and thioacetyl substituents for nucleic acid detection

Fifteen novel mono-, di- and tricationic monomeric monomethine cyanine dyes, bearing mercapto and thioacetyl substituents, useful for nucleic acid detection are described. All derivatives absorb in the region 417–508 nm and have molar absorptivities of 61 000–101 300 l mol −1 cm −1. The products were characterized by 1H NMR, HPLC–MS and elemental analysis.

Effect of Laponite and a Nonionic Polymer on the Absorption Character of Cationic Dye Solutions

The effect of Laponite and an amphiphilic triblock copolymer of poly(ethylene oxide) (PEO)-poly(propylene oxide) (PPO)-poly(ethylene oxide) (PEO) (PEO(99)-PPO(65)-PEO(99), and labeled F127) on the absorption character of two cationic dyes, methylene blue and toluidine blue O, was studied and interpreted in terms of the changing state of aggregation of the dye molecules. The combined effect of the polymer and Laponite on dye absorption was significantly different from their individual influences. Specifically, the presence of Laponite resulted in an increase in monomer population by dispersing the dye on the silicate surface. The presence of F127 also resulted in an increase in the dye monomer population, although to a smaller extent. The combined effect of the polymer and Laponite was an increase in the dimer or aggregate populations attributed to the competition of F127 with the dye molecules for the silicate surface.

Aggregation behavior of the red-absorbing oxazine derivative MR 121: A new method for determination of pure dimer spectra

In this Letter, we investigated the dimerization behavior of the red-absorbing oxazine derivative MR121. Thereby a new method to determine absorption spectra of pure non-fluorescent H-type dye dimers is presented. Therefore, the amino acid lysine is doubly labeled with the fluorescent dye in order to obtain an absorption spectrum mainly caused by dimers. By subtracting the fraction arising from monomeric dye, the dimer spectrum is generated. The extinction coefficient at absorption maximum (608 nm) was estimated to be 86 000 ± 2000 M −1 cm −1 per dye. Furthermore, the equilibrium constant K D for the dimerization reaction is determined to be 3300 ± 300 M −1.

Formation of Monomeric and Novolak Azo Dyes in Nanofluid Segments by Use of a Double Injector Chip Reactor

AbstractThe azo coupling of 2‐naphthol and cresol novolaks was performed as an example for organic reactions in a microsegmented flow system with microspectrophotometric on‐line characterization. A lithographically prepared glass/glass chip microreactor was used for the generation of segments and the mixing of reaction partners. The formation of segments and their transport behavior is strongly influenced by the addition of surfactants. The reaction rates were high in alkaline media at room temperature, so that the formation of dyes could be observed by a microscope‐video system. The single reaction volumes were in the range between about 0.05 and 1 μL. The spectrum of each segment was registered with a measuring frequency of 45–50 Hz. The residence time of segments inside the optical measurement channels varied between 0.1 and 1.5 s and is in the range of 0.3 s for typical segment sizes of about 150 nL. The single reaction segments containing azo dyes as well as polymer‐based azo dyes were stored in segment sequences inside capillary Teflon tubes.

Dye Sensitization of the Anatase (101) Crystal Surface by a Series of Dicarboxylated Thiacyanine Dyes

Dye sensitization of the single crystal anatase (101) surface was studied using a structurally similar series of dicarboxylated thiacyanine dyes that bind to the oxide surface through their carboxylate groups. An ultraviolet (UV) light treatment of the anatase (101) surfaces, immediately prior to dye adsorption, improved both the reproducibility of dye coverage and the incident photon-to-current efficiencies (IPCE) for sensitization. The UV treatment does not pit or roughen the anatase surface and results in high IPCEs of more than 1% in some cases and absorbed photon current efficiencies (APCE) from 5 to 100%. The photocurrent spectra showed features associated with surface-bound dye monomers and H-dimers that could be followed as a function of the dye surface coverage. Models for the surface structures of the adsorbed dye layers that are consistent with the measurements are presented, along with a discussion of adsorption isotherms.

Self Assembly of Cyanine Dye on Clay Nanoparticles

The effect of Ca-montmorillonite (clay) on the aggregation behavior of the cyanine dye, 1,1’-diethyl-2,2’-cyanine iodide (PIC), in aqueous solutions has been investigated using UV-vis spectroscopy. The absorbance of the monomeric dye in aqueous solutions is compared with the absorbance of the aggregates formed after adding the clay. The appearance of a sharp “red-shifted” band centered at 574 nm, after the addition of clay to the aqueous solutions of the dye, indicates the formation J-aggregates on the charged surfaces of the clay particles. The spontaneous and quantitative transformation of monomers into J-aggregates was controlled by the concentration of the clay in the solution. Successive addition of clay to the dye solution causes an increase in the absorbance intensity of the J-band and consequently, a decrease in the absorbance intensity of the monomer. These changes occur linearly which suggests that the dye monomers are quantitatively being converted to J-aggregates.

Investigation of Conformational and Electron Properties of Biscyanine Dyes

ABSTRACT The spectral and luminescent characteristics of four biscyanine dyes and corresponding monomer dye in ethanol solutions and in polyvinyl butyral have been investigated. The influence of angle between chromophores of biscyanine molecules on splitting and intensity of absorption bands has been discussed. It has been shown that the splitting of the biscyanine excited electron level S1 is caused both dipole and resonant chromophor interactions. It has been found that the fluorescence quantum yields of the biscyanines in ethanol at room temperature are 0.005–0.02. The introduction of biscyanines in a polymer matrix, which provides rigidity of a polymethine chain, results in reduction of molecules trans-cis isomerization and consequently increase of fluorescence quantum yields.

Molecular Orientation of Rhodamine Dyes on Surfaces of Layered Silicates

Films of the layered silicates fluorohectorite (FH) and saponite (Sap) with various rhodamine dyes were prepared. The dyes with acidic as well as large hydrophobic groups in their molecule were not adsorbed on the surface of FH, which was interpreted in terms of high charge density on the surface of this silicate. All adsorbed dyes formed similar forms, such as isolated cations and H-type molecular aggregates, which were characterized by different spectral properties. Polarized ultraviolet-visible (UV-vis) spectroscopy was used for the characterization of the molecular orientation of dye chromophores on the silicate surface. The isolated dye cations and species, which absorbed light at the low energy part of the spectra, were only slightly tilted with respect to the plane of the silicate surface. The cations forming H-aggregates and absorbing light at low wavelengths were oriented in a nearly perpendicular fashion. The nearly perpendicular orientation was observed as a strong increase of dichroic ratio with film tilting. The orientation of the cations in H-aggregates depends partially on the structure of the dye molecule, namely, on the type of amino group (primary, secondary, or tertiary) in the dye molecule. The type of amino groups probably plays a role in the suitable orientation of dye cations for effective electrostatic interaction between the cations and the negatively charged siloxane surface. X-ray powder diffraction could not distinguish dye phases of dye monomers and molecular aggregates.

J-Aggregates of Cyanine Dyes in Aqueous Solution of Polymers: A Quantitative Study

The effect of polyvinylsulfate (PVS) on the spectroscopy of the cyanine dye, 1,1’-diethyl-2,2’-cyanine iodide (PIC), has been investigated using UV-vis spectroscopy. J-aggregates of the PIC dye were formed upon addition of PVS to the monomers of the dye in solution. The appearance of only one isosbestic point in the UV-vis spectra suggests that the dye monomers are quantitatively converted to J-aggregates and equilibrium was reached. Using Benisi-Hildebrand kinetics, aggregation number of 4 was calculated for the dye. In addition, a 1:2 mole ratio of PIC/PVS was calculated at the maximum capacity of the polymer.

Fluorescence of acridinic dyes in anionic surfactant solution

The interaction of the cationic dyes acridine, 9-aminoacridine (9AA), and proflavine, with sodium dodecyl sulfate (SDS) was studied by electronic absorption, steady-state and time-resolved fluorescence spectroscopies. The dyes interact with SDS in the pre-micellar region leading in two cases to dimerization in dye–surfactant aggregates, but with distinct molecular arrangements. For proflavine, the observed red shift of the electronic absorption band indicates the presence of J-aggregate, which are nonfluorescent. In the case of 9AA, the aggregates were characterized as nonspecific (neither J- nor H-type is spectroscopically observed). The time-resolved emission spectra gives evidences of the presence of weakly bound dimers by the recovery of three defined decay times by global analysis: dye monomer ( τ 1 = 16.4 ns), dimer ( τ 2 = 7.1 ns), and a faster component ( τ 3 = 2.1 ns) ascribed to intracluster energy migration between monomer and dimer. Acridine has a weak interaction with SDS forming only an ion pair without further self-aggregation of the dye.

Synthesis of novel monomeric and homodimeric cyanine dyes based on oxazolo[4,5- b]pyridinium and quinolinium end groups for nucleic acid detection

Twelve novel di-, tri- and tetracationic monomeric and homodimeric monomethine cyanine dyes based on oxazolo[4,5- b]pyridinium and quinolinium end groups were synthesized by condensation of 4-methyl-2-methylmercapto-oxazolo[4,5- b]pyridinium methosulfate and 1-(ω-iodopropyl)-4-methylquinolinium or appropriate 1-(ω-bromoalkyl)-4-methylquinolinium compounds and subsequent quaternization with pyridine, 1-methyl-4-aza-1-azonia-bicyclo[2.2.2]octanium iodide, 4,4′-trimethylenebis(1-methylpiperidinium)methyl iodide, N,N,N,N′, N′-pentamethyl-1,3-propandiammonium iodide, or bisquaternization with N,N,N′, N′-tetramethyl-1,3-propanediamine, 4,4′-trimethylenebis(1-methylpiperidine). All dyes absorb at 521–522 nm in methanol and have a high molar absorptivity of about 106 000 (monomeric dyes) and 240 000 L mol −1 cm −1 (homodimeric dyes). The products were characterized by 1H NMR spectra and elemental analysis. In the presence of nucleic acid a strong enhancement of the fluorescence was observed.

Coupled Electron‐Proton Transport in Electropolymerized Methylene Blue and the Influences of Its Protonation Level on the Rate of Electron Exchange with β‐Nicotinamide Adenine Dinucleotide

AbstractThis paper describes electrochemical characteristics of poly(methylene blue) electrolytically deposited on glassy carbon and examines the electrocatalytic activity of the polymer toward oxidation of the coenzyme NADH. Redox‐active properties of the cationic polyelectrolyte arose from both electron self‐exchange between electroactive sites and a high ionic film‐conductivity. The diffusion coefficient of charge carriers in the film increased with decreasing solution pH, indicating the pH dependence of the electron diffusion coefficient. The electrocatalytic oxidation of NADH at the polymer‐modified electrode proceeded via an intermediate charge‐transfer complex of the reduced polymer with the oxidized coenzyme. The complex dissociated more rapidly into the oxidation products as the reduced polymer protonated. Thus, the rate constant for the cross‐exchange reaction rose with a decrease in pH. For NADH oxidation, the polyelectrolyte exhibited an electrocatalytic activity higher than the monomeric dye because of a stronger oxidizing power of the second oxidized form of the polymer.

Spectroscopic studies of β-cyclodextrin-complexed cyanine dyes

We have studied the interaction of a homologous series of symmetrical thiacyanine dyes (DTCI, DTDCI, DTTCI) with β-cyclodextrin. From absorption spectra we infer that all three dyes form β-CD complexes, either as dye cation monomer or dimer. Higher aggregates, e.g. H-aggregates, are observable in water alone for both DTDCI and DTTCI, as is well-known. The H-aggregate formed from DTTCI in water provides evidence of a unique pathway for thermalization of photoexcitation energy; excited aggregate ejects excited dye monomer. β-CD complexes of all three dyes exhibit technologically useful levels of second-order hyperpolarizability, measured by Hyper-Rayleigh scattering, and we assign the non-linear optical response to dimer complex. Second-order scattering is observed, however, only when the saturation concentration of dye monomer in water is exceeded; at lower concentrations we infer that complexes do not form. Computational modelling, carried out for DTCI, suggests that the dimer forms endergonically with a structure that both locks in a significant degree of bond alternation, as well as allowing considerable freedom for torsional relaxation.

The aggregation of thionine and methylene blue dye in smectite dispersion

Interaction of cationic dyes, thionine (Th) and methylene blue (MB), with smectites in the aqueous dispersions was investigated using visible spectroscopy. Smectite samples of various layer charge were used: low-charge laponite (Lap), middle-charge Kunipia F montmorillonite (Kun) and high-charge fluorohectorite (FH). Dyes cations formed monomers, dimers and larger-size aggregates of H-type (sandwich type) and in a few cases of J-type (head-to-tail association). Each form of the dye was identified using visible (VIS) spectroscopy. The effects of layer charge, the type of the dye and smectite, and the influence of dye/clay ratio on the formation of specific dye species were compared. Negligible influence of the dye loading was observed for most cases, being always much lower than the effect of the layer charge density. Dye/Lap reaction systems were dominated by isolated dye cations. H-dimers and larger-size molecular aggregates were formed on the surface of this clay only at the highest loading tested (0.50 mmol/g). On the other hand, the reaction systems with a middle-charge Kun montmorillonite contained roughly equal amounts of dye monomers and H-aggregates at low loadings and slightly more H-aggregates were formed at high loadings. The spectra of dye/FH reaction systems were always dominated by the bands assigned to H-aggregates. The surface of high-charge densities induced destabilization and decomposition of Th cations especially at high dye concentrations on clay surface. The effects of silicate structure and composition on the optical properties of adsorbed dyes were not identified.

The rhodamine B intercalation of montmorillonite

Using photometric methods the dissociation constants and weight fractions of rhodamine B dimer in water solutions at different concentrations were determined. The montmorillonite (SWy) samples were fully intercalated with rhodamine B (RhB) solutions at various monomer/dimer ratios. The amount of rhodamine B in fully intercalated montmorillonite (RhB–SWy) increases with increasing concentration of dye in water solutions, i.e., with increasing dimer/monomer ratio. The sum of exchangeable guest cations in RhB–SWy is approximately constant (0.900 meq g−1) for all samples, because RhB–SWy samples with prevailing dye monomer also contain higher amounts of non-exchanged alkali elements. The experimental data are supported by calculated structure models that illustrate the changes in RhB–SWy structure depending on monomeric and/or dimeric arrangement of guests. The analysis of the calculated structure models confirmed the existence of two phases with different basal spacings, d∼1.8 and ∼2.3 nm, revealed by X-ray diffraction.

The polarization of fluorescence of DNA stains depends on the incorporation density of the dye molecules.

The fluorescence induced by polarized light sources, such as the lasers that are used in flow cytometry, is often polarized and anisotropic. In addition, most optical detector systems are sensitive to the direction of polarization. These two factors influence the accuracy of fluorescence intensity measurements. The intensity of two light sources can be compared only if all details of the direction and degree of polarization are known. In a previous study, we observed that fluorescence polarization might be modified by dye-dye interactions. This report further investigates the role of dye density in fluorescence polarization anisotropy. We measured the polarization distribution of samples stained with commonly used DNA dyes. To determine the role of fluorophore proximity, we compared the monomeric and a dimeric form of the DNA dyes ethidium bromide (EB), thiazole orange (TO), and oxazole yellow (YO). In all dyes sampled, fluorescence polarization is less at high dye concentrations than at low concentrations. The monomeric dyes exhibit a higher degree of polarization than the dimeric dyes of the same species. The polarization of fluorescence from DNA dyes is related to the density of incorporation into the DNA helix. Energy transfer between molecules that are in close proximity loosens the linkage between the excitation and emission dipoles, thereby reducing the degree of polarization of the emission.

Supramolecular polymerization and gel formation of bis(merocyanine) dyes driven by dipolar aggregation.

Two highly dipolar merocyanine dyes were tethered by a rigid tris(n-dodecyloxy)xylylene unit that preorganizes the dyes for a supramolecular polymerization process through intermolecular aggregation of the dyes. UV/vis spectroscopy revealed a solvent dependent equilibrium between monomeric dyes and two different types of dye aggregates that are characterized by hypsochromically shifted D- and H-type absorption bands. Taking into account the ditopic nature of the supramolecular building blocks, the occurrence of the D-band indicates the formation of an oligomeric/polymeric supramolecular chain whereas the observation of the H-band suggests a higher order assembly. For the H-aggregated dyes, intrinsic viscosities exceed 0.65 L g(-1) in methylcyclohexane, values typically found for macromolecular solutions. At higher concentration, further association of these aggregates takes place by entanglement of the alkyl groups leading to a substantial increase in viscosity and gelation. Rheology studies show linear viscoelastic behavior which was attributed to the formation of an entangled dynamic network. AFM and cryo-TEM studies of the gel reveal long and stiff rod-type assemblies. X-ray diffraction studies for a solid film show columnar mesomorphism. Based on these results, a structural model is proposed in which six helically preorganized strands of the supramolecular polymer intertwine to form a rod with a diameter of about 5 nm. Within these rods all dyes are tightly aggregated in a tubular fashion giving rise to delocalized excitonic states, and the pi-conjugated tube is jacketed by the tridodecyloxy groups.