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.     

Effects of Amino Group Substitution on the Photophysical Properties and Stability of Near-Infrared Fluorescent P-Rhodamines

A series of phosphine oxide-bridged rhodamines (P-rhodamines) bearing various acyclic and cyclic amine moieties, including dimethyl- and diethylamine, azetidine, pyrrolidine and 7-azabicyclo[2,2,1]heptane (7ABH), have been synthesized. The photophysical properties as well as chemical and photostability of these dyes have been studied in detail. Among these dyes, the 7ABH-substituted dye shows stronger fluorescence in the near-infrared (NIR) region, relative to the other P-rhodamines. This dye could be applied to live-cell imaging, wherein lysosomes were selectively stained in a pH-independent manner. It was also found that the ring fusion of the amine moieties gives rise to remarkably redshifted spectra, with absorption and emission maxima at 770 and 820 nm, respectively, spectrally close to that of indocyanine green (ICG). Importantly, the ring-fused P-rhodamines showed much higher photostability than ICG, indicative of their promising utility as the NIR-emissive dyes.     

Spectral Förster resonance energy transfer detection of protein interactions in surface-supported bilayers

F?rster resonance energy transfer (FRET), a fluorescence detection technique, is often used for sensing molecular interactions in solution and in membranes. Here we show that (1) FRET spectra can be recorded in single bilayers, supported on a surface, and (2) the fluorescein/rhodamine dye pair is an adequate reporter of FRET when spectral detection is used. Thus, measurements pertaining to molecular interactions in membranes can be carried out in supported bilayers. Spectral FRET has advantages over imaging FRET, which monitors only signal amplitudes at certain wavelength. There are also advantages to performing spectral FRET measurements in supported bilayers as compared to free liposomes in suspension. However, the spectral properties of dyes can be altered in an unexpected manner in an ordered bilayer structure on a surface, such that fluorescence detection in surface-supported bilayers is not always trivial.     

Heteroatom-substituted rhodamine dyes: Structure and spectroscopic properties

Rhodamine is one class of most popular dyes used in fluorescence imaging due to the outstanding photoproperties including high brightness and photostability. In recent years, replacement the xanthene oxygen with other elements, especially silicon, has attracted great attentions in the development of new rhodamine derivatives. This review summarized the structures and photophysical properties of heteroatom-substituted rhodamines. We hope this review can help to understand the structure-property relationships of rhodamine dyes and then elucidate the way to create derivatives with improved photoproperties.     

Triangular Rhodamine Triads and Their Intrinsic Photophysics Revealed from Gas-Phase Ion Fluorescence Experiments

When ionic dyes are close together, the internal Coulomb interaction may affect their photophysics and the energy-transfer efficiency. To explore this, we have prepared triangular architectures of three rhodamines connected to a central triethynylbenzene unit (1,3,5-tris(buta-1,3-diyn-1-yl)benzene) based on acetylenic coupling reactions and measured fluorescence spectra of the isolated, triply charged ions in vacuo. We find from comparisons with previously reported monomer and dimer spectra that while polarization of the π-system causes redshifted emission, the separation between the rhodamines is too large for a Stark shift. This picture is supported by electrostatic calculations on model systems composed of three linear and polarizable ionic dyes in D_3h configuration: The electric field that each dye experiences from the other two is too small to induce a dipole moment, both in the ground and the excited state. In the case of heterotrimers that contain either two rhodamine 575 (R575) and one R640 or one R575 and two R640, emission is almost purely from R640 although the polarization of the π-system expectedly diminishes the dipole-dipole interaction.     

Heteroatom-substituted rhodamine dyes: Structure and spectroscopic properties

This review summarized the structures and photophysical properties of heteroatom-substituted rhodamines.     

Synthesis of a Far‐Red Photoactivatable Silicon‐Containing Rhodamine for Super‐Resolution Microscopy

The rhodamine system is a flexible framework for building small‐molecule fluorescent probes. Changing N‐substitution patterns and replacing the xanthene oxygen with a dimethylsilicon moiety can shift the absorption and fluorescence emission maxima of rhodamine dyes to longer wavelengths. Acylation of the rhodamine nitrogen atoms forces the molecule to adopt a nonfluorescent lactone form, providing a convenient method to make fluorogenic compounds. Herein, we take advantage of all of these structural manipulations and describe a novel photoactivatable fluorophore based on a Si‐containing analogue of Q‐rhodamine. This probe is the first example of a “caged” Si‐rhodamine, exhibits higher photon counts compared to established localization microscopy dyes, and is sufficiently red‐shifted to allow multicolor imaging. The dye is a useful label for super‐resolution imaging and constitutes a new scaffold for far‐red fluorogenic molecules.     

Synthesis of rhodamines from fluoresceins using Pd-catalyzed C-N cross-coupling

A unified, convenient, and efficient strategy for the preparation of rhodamines and N,N'-diacylated rhodamines has been developed. Fluorescein ditriflates were found to undergo palladium-catalyzed C-N cross-coupling with amines, amides, carbamates, and other nitrogen nucleophiles to provide direct access to known and novel rhodamine derivatives, including fluorescent dyes, quenchers, and latent fluorophores.     

The optical properties of molecules and chromogenic aggregates of xanthene dyes

The UV absorption spectra of rhodamine B and G molecules isolated from industrial dye samples were obtained. Two procedures were used. In one of them, rhodamine B molecules were displaced with water into a heptane layer from a solution of the dye in an alcohol-heptane mixture. The second procedure involved heating of the dye introduced into cellulose triacetate films. Individual rhodamine molecules (namely, dye cation-chlorine anion ion pairs) prepared by both methods did not absorb visible light. The spectra of individual rhodamine molecules coincided with the spectra of so-called pseudoleucobases of xanthene dyes reported in the literature. The conclusion was drawn that the chromaticity property in the series of xanthene dyes appeared because of the formation of supramolecular dimeric and larger aggregates, as was earlier established for triphenylmethane dyes (TPMDs) and copper phthalocyanine (CuPc). At the same time, individual xanthene dye molecules, like TPMD and CuPc molecules, are not chromogens.     

Spectroscopic studies of a near-infrared absorbing pH sensitive aminodienone-carbocyanine dye system

Synthetic red and near-infrared absorbing dyes may be used as probe molecules in a large number of applications. Dyes exhibiting spectral changes with hydrogen ion concentration are useful as pH probes. Those dyes which have their absorption and fluorescence maxima in the long wavelength region of the visible spectral region are specially valuable because of decreased interference and semiconductor laser applications. In this paper we have evaluated an aminodienone dyes 1 which demostrates pH dependent absorption and fluorescence spectra as well as solvent polarity dependence. In organic solvents the long wavelength absorption band of the dye is in the reduced interference region. The absorption maximum is at 535 nm in neutral or alkaline solutions in methanol. The absorption spectra undergo a strong bathochromic shift in the presence of acids (lambda(max) = 709 nm) with a concomitant change in the fluorescence spectra. This pH sensitive dye was found to be specially especially useful for organic solvents. The analytical utility of this and similar near-infrared absorbing dyes is discussed.     

Absorption spectroscopic investigation of rhodamine dye vapors

The dyes rhodamine 6G and rhodamine 19 are investigated. The dye stability versus temperature and time is studied. Bulk dye stuff is found to be less stable than dye adsorbed to the stainless steel cell walls and in the vapor phase. Rhodamine 6G converts to rhodamine 19 before evaporation. Adsorbed rhodamine 19 and rhodamine 19 vapor disintegrate most likely into 2,7-dimethylrhodamine 110 at elevated temperatures (> 320°C). For rhodamine 19 vapor the absorption spectrum, the saturated vapor density and the latent heat of evaporation are determined. The vapor absorption spectra of rhodamine 19 and 2,7-dimethylrhodamine 110 are compared with solution spectra.     

Influence of the molecular structure and the nature of the solvent on the absorption and fluorescence characteristics of rhodamines

A study of the equilibrium of the molecular forms of rhodamine 19 in aqueous and ethanolic solution is carried out by determining the absorption and fluorescence characteristics of the zwitterionic and the cationic forms of the dye. The optical properties of rhodamine 19 are compared with those obtained for rhodamine 6G and also with those previously reported for rhodamine 3B and for the molecular forms of rhodamine B in water and ethanol. Different aspects of the molecular structure of the rhodamines and solvent effects are discussed, as well as their influence on the photophysical properties of the rhodamines. The aggregation of the molecular forms of rhodamine 19 is also studied in water and ethanol.     

Vibrational spectra of the excited electronic state of rhodamine molecules obtained by cars spectroscopy

CARS spectra of the ground and an excited electronic state of rhodamine dyes are observed under two different resonance conditions using nanosecond dye lasers The observed differences are not due to structural changes.     

Far‐Red Emitting Fluorescent Dyes for Optical Nanoscopy: Fluorinated Silicon–Rhodamines (SiRF Dyes) and Phosphorylated Oxazines

Far‐red emitting fluorescent dyes for optical microscopy, stimulated emission depletion (STED), and ground‐state depletion (GSDIM) super‐resolution microscopy are presented. Fluorinated silicon–rhodamines (SiRF dyes) and phosphorylated oxazines have absorption and emission maxima at about λ≈660 and 680 nm, respectively, possess high photostability, and large fluorescence quantum yields in water. A high‐yielding synthetic path to introduce three aromatic fluorine atoms and unconventional conjugation/solubilization spacers into the scaffold of a silicon–rhodamine is described. The bathochromic shift in SiRF dyes is achieved without additional fused rings or double bonds. As a result, the molecular size and molecular mass stay quite small (<600 Da). The use of the λ=800 nm STED beam instead of the commonly used one at λ=750–775 nm provides excellent imaging performance and suppresses re‐excitation of SiRF and the oxazine dyes. The photophysical properties and immunofluorescence imaging performance of these new far‐red emitting dyes (photobleaching, optical resolution, and switch‐off behavior) are discussed in detail and compared with those of some well‐established fluorophores with similar spectral properties.     

Rational design of far red to near-infrared rhodamine analogues with huge Stokes shifts for single-laser excitation multicolor imaging

Rhodamine dyes have been widely employed in biological imaging and sensing. However, it is always a challenge to design rhodamine derivatives with huge Stokes shift to address the draconian requirements of single-excitation multicolor imaging. In this work, we described a generally strategy to enhance the Stokes shift of rhodamine dyes by completely breaking their electronic symmetry. As a result, the Stokes shift of novel rhodamine dye DQF-RB-Cl is up to 205 nm in PBS, which is the largest in all the reported rhodamine derivatives. In addition, we successfully realized the single excitation trichromatic imaging of mitochondria, lysosomes and cell membranes by combining DQF-RB-Cl with commercial lysosomal targeting probe Lyso-Tracker Green and membrane targeting dye Dil. This is the organic synthetic dyes for SLE-trichromatic imaging in cells for the first time. These results demonstrate the potential of our design as a useful strategy to develop huge Stokes shift fluorophore for bioimaging.     

Surface- and resonance-enhanced micro-Raman spectroscopy of xanthene dyes: from the ensemble to single molecules.

Surface-enhanced resonance Raman scattering (SERRS) spectra of various rhodamine dyes, of pyronine G and thiopyronine adsorbed on isolated silver clusters were recorded at the ensemble level and at the single-molecule level with a high-resolution confocal laser microscope equipped with a spectrograph and a CCD-detector. Comparing single-molecule spectra with ensemble spectra, various inhomogeneous spectral features, such as line splitting, spectral wandering, spectral diffusion and abrupt spectral jumps between different metastable spectral states, are revealed positions and the relative intensities of the vibronic bands. Resonance enhancement is investigated with respect to single-molecule surface-enhanced Raman scattering (SERS) spectroscopy and is found to be responsible for approximately three orders of magnitude in sensitivity. A significant influence of the substituents on the single-molecule SERRS sensitivity is found, showing that various chemical effects are responsible for surface enhancement in addition to the electromagnetic enhancement effect.     

Molecular aggregation of rhodamine dyes in dispersions of layered silicates: influence of dye molecular structure and silicate properties

The molecular aggregation of six rhodamine dyes (rhodamine 560, B, 3B, 19, 6G, 123) in layered silicate (saponite and fluorohectorite) dispersions was investigated by using visible (vis) spectroscopy. The dye molecular aggregation was influenced by the properties of both the silicates and the dyes themselves. The layer charge of the silicates enhanced the molecular aggregation of the hydrophilic, cationic dyes. The presence of a carboxyl acid group in the dye molecules inhibited adsorption of the dyes on the surface of fluorohectorite, a silicate with a high charge density. A lower or no adsorption could be observed by vis spectroscopy. Strong association of the dyes to the silicate surface led to remarkable changes in the dye spectra, mainly due to the molecular aggregation. Dye assemblies initially formed after mixing the dye solutions with silicate dispersions were unstable. Decomposition of the dye molecular assemblies, and the formation of new species or molecular aggregate rearrangements, were studied on the bases of time-difference spectra. The reaction pathways were specific, not only for the dyes, depending upon their molecular structure and properties, but also on the silicate substrates.     

Evaluation of the reduction of imidazophenazine dye derivatives under fast-atom-bombardment mass-spectrometric conditions

Satellite [M + 2](+*) and [M + 3](+) peaks accompanying the common peak of the protonated molecule [M + H](+) that are known to indicate the occurrence of a reduction process were observed in the fast atom bombardment (FAB) mass spectra of imidazophenazine dye derivatives in glycerol matrix. The distribution of the abundances in the [M + nH](+) peak group varied noticeably for different derivatives. This indicated different levels of the reduction depending on the different structure variations of the studied molecules. In the search for correlations between the mass spectral pattern and the structural features of the dyes, ab initio HF/6-31++G** quantum chemical calculations were performed. They revealed that the abundances of the [M + 2](+*) and [M + 3](+) ions show growth proportional to the decrease of the energy of the lowest unoccupied molecular orbital, i.e. proportional to the increase of the electron affinity of the dye molecule. A method for rapid screening of reductive properties of sets of dye derivatives on the basis of the FAB mass spectral data is discussed.     

A Highly Photostable Near‐Infrared Labeling Agent Based on a Phospha‐rhodamine for Long‐Term and Deep Imaging

Various fluorescence microscopy techniques require bright NIR‐emitting fluorophores with high chemical and photostability. Now, the significant performance improvement of phosphorus‐substituted rhodamine dyes (PORs) upon substitution at the 9‐position with a 2,6‐dimethoxyphenyl group is reported. The thus obtained dye PREX 710 was used to stain mitochondria in living cells, which allowed long‐term and three‐color imaging in the vis‐NIR range. Moreover, the high fluorescence longevity of PREX 710 allows tracking a dye‐labeled biomolecule by single‐molecule microscopy under physiological conditions. Deep imaging of blood vessels in mice brain has also been achieved using the bright NIR‐emitting PREX 710‐dextran conjugate.     

Quick monitoring of coloring agents in highly consumed candies using multivariate calibration

Multivariate calibration are gaining popularity in assaying food matrices. Partial least squares is a powerful multivariate calibration method that used to build a quantitative relationship between measured variables and a property of interest (i.e., concentration) of the system under study. Partial least squares PLS calibration along with UV/vis spectral data was efficient to account for indirect food matrix and direct interference effects resulted from overlapping food dyes. PLS was able to quantify tartrazine TAT, allura red AR, sunset yellow SY and brilliant black BB that added to wide selection sugar-based candies. The results indicated that 70% of samples containing single dye while 8% containing TAT-SY mix and certain samples containing TAT + SY + AR + BB. Lollypops were found to contain high levels of AR (77–120 mg/kg) and TAT (56–166 mg/kg). The maximum adulteration was 50% observed in lollypops. PLS calibration was workable to predict colorants with prediction errors of 7%. Using PLS, dyes were detected down to 0.1 mg/L with acceptable accuracy and precision. PLS showed comparable performance with liquid chromatography for dyes quantification and can substitute laborious chromatography for quick detection of coloring agents in candies.