The Stokes-shifted fluorescence risetime of dye molecules in solution

We have measured the rise of Stokes-shifted spontaneous fluorescence intensity during a 10 ps 530 nm actinic light pulse for rhodamine B, rhodamine 6G and erythrosin B dissolved in water, ethanol and methanol. The best numerical fit to our data corresponds to a time delay of less than 1 ps between excitation and fluorescence emission.     

Characterizing the fluorescence intermittency and photobleaching kinetics of dye molecules immobilized on a glass surface

The blinking behavior of single Atto565 molecules on a glass surface is studied under air or nitrogen atmospheres using confocal microscopy. The broad distributions for both on- and off-time durations obey power law kinetics that are rationalized using a charge tunneling model. In this case, a charge is transferred from the Atto565 molecule to localized states found on the glass surface. Subsequent charge recombination by back charge tunneling from trap to Atto565 cation (i.e., dark state) restores the fluorescence. The off-time distribution is independent of excitation intensity (I), whereas the on-time distribution exhibits a power law exponent that varies with I. Two pathways have been identified to lead to the formation of the radical dark state. The first involves direct charge tunneling from the excited singlet S1 state to charge traps in the surrounding matrix, and the second requires charge ejection from the triplet T1 state after intersystem crossing from S1. Monte Carlo simulation studies complement the two-pathway model. Photobleaching curves of both single and ensemble molecules do not exhibit monoexponential decays suggesting complex bleaching dynamics arising from triplet and radical states.     

Study of the adsorptive behavior of water-soluble dye molecules (rhodamine 6G) at the air-water interface using confocal fluorescence microscope

A confocal fluorescence microscope was applied to directly study the characteristic behaviors of adsorbed molecules at the air-water interface for a water-soluble chromophore, rhodamine 6G (R6G), in its extremely low-concentration region (below 10(-10) M). Significant photon bursts were observed only from the surface, and their width, height, and frequency were found to depend on the bulk concentration, suggesting the inhomogeneous distribution of R6G molecules at the air-water interface. This property of the adsorbed molecules is different from that of the bulk one. The influence of the ionic strength on photon bursts from the interface was investigated. It was found that the addition of NaCl to the R6G solution caused a decrease of the fluorescence signal. A change in the size of the aggregate and in the fluorescence quantum yield of the adsorbed molecules was suggested to be responsible for this experimental result.     

The estimation of reaction enthalpy for complex molecules using Benson groups</o:p>

Estimation methods developed over years by S. W. Benson and co-workers for calculation the thermodynamic properties of organic compounds in the gas phase are applied to a pharmaceutical real process with all type of non-idealities. The different strategies used to calculate the reaction enthalpy of a chemical process, in the absence of data for complex molecules, using the Benson group additivity method are presented and also compared with the experimental value of reaction enthalpy obtained using reaction calorimetry (Mettler-Toledo, RC1?). We demonstrate that there are some strategies that can be followed to obtain a good estimation of the reaction enthalpy in order to begin the safety assessment of a chemical reaction. This work is part of an industrial project [1] in which the main objective was the risk assessment of chemical real and complex processes using the commonly available tools for the SMEs (with limited resources).     

Capillary electrophoresis of double-stranded DNA fragments using a new fluorescence intercalating dye EvaGreen

EvaGreen is a new DNA intercalating dye successfully used in quantitative real-time PCR. In the present work, we firstly apply EvaGreen to the analysis of dsDNA by CE with LIF detection. Comparisons of EvaGreen dye with the commonly used dyes SYBR Green I and SYBR Gold were preformed in dsDNA analysis by CE. The linear range of dsDNA using EvaGreen was slightly wider than that using SYBR Gold and SYBR Green I, and the detection limits of dsDNA were not significantly different for the three dyes. Good separations of dsDNA fragments were obtained using the three dyes. Reproducibility of migration time and the peak area of dsDNA fragments with EvaGreen were better than those for SYBR Green I and SYBR Gold. The RSD values were 0.24-0.27% for migration time and 3.45-7.59% for peak area within the same day, 1.35-1.63% for migration time and 6.72-12.05% for peak area for three days. Our data demonstrated that EvaGreen is well suited for the dsDNA analysis by CE with LIF detection.     

Reduced fluorescence quenching of cyclodextrin-acetylene dye rotaxanes

An acetylene dye rotaxane with alpha-CD has been synthesized using the Heck-Cassar-Sonogashira-Hagihara-type reaction in aqueous solution. Free dye with tetracarboxylic acids is found to be highly sensitive to various metal ions, showing high Stern-Volmer constants, KSV. As CD encapsulation protects and stabilizes the threaded chromophore against an outside quencher, metal-insensitive biological tags are an obvious application for this class of molecules.     

Effect of pressure on viscosity-dependent dye fluorescence

The fluorescence of the dyes crystal violet, auramine-O and eosin-Y has been studied as a function of pressure in glycerol and polyvinylalcohol at room temperature. The strong pressure sensitivity observed for the substituted methane dyes is related to the viscosity change of the fluid medium.     

Absorption and fluorescence of single molecules

Simultaneous detection of single molecules by absorption and fluorescence is demonstrated using confocal microscopy at cryogenic temperature. Dynamical processes such as blinking and spectral jumping of single emitters are observed in both detection channels. The relative magnitude of fluorescence and absorption varies between molecules. In particular, we observe molecules that do not emit detectable Stokes-shifted fluorescence but show a strong absorption signal. The fact that coherent resonant scattering underlies the absorption process is demonstrated by a correlation between small linewidth and large absorption amplitude.     

Structuring of tricarbocyanine dye molecules in Langmuir-Blodgett films

The problems of formation of stable Langmuir monolayers containingN-sulfopropyl substituted thiatricarbocyanine dyes are considered: the effects of the composition of the mixture applied on the surface of an aqueous subphase and of the extent of compression of the monolayer on processes of ordering of molecular structure. Dyes are introduced into complex monolayers at the water-air interface and then are transferred on solid substrates as multilayered Langmuir-Blodgett (LB) films. For the first time the formation of J-aggregates has been observed for two tricarbocyanine dyes. The structure of J-aggregates depends on the composition of the mixture and the value of the constant pressure at which the transfer occurs. LB films of J-aggregated dyes are optically anisotropic, which is related to the fact that they are formed in the monolayer on the surface and there is no interlayer aggregation during the transfer to substrates. Heterodimers are formed in complex monolayers containing oppositely charged ions of dyes.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1278–1283, July, 1995.The work was partially financially supported by the Foundation for Basic Research of the State Committee on Science and Technologies of the Ukraine (Project No. 2.2/48 Normal').     

Synchronous fluorescence spectroscopic study of solvatochromic curcumin dye

Curcumin, the main yellow bioactive component of turmeric, has recently acquired attention by chemists due its wide range of potential biological applications as an antioxidant, an anti-inflammatory, and an anti-carcinogenic agent. This molecule fluoresces weakly and poorly soluble in water. In this detailed study of curcumin in thirteen different solvents, both the absorption and fluorescence spectra of curcumin was found to be broad, however, a narrower and simple synchronous fluorescence spectrum of curcumin was obtained at Δλ=10-20 nm. Lippert-Mataga plot of curcumin in different solvents illustrated two sets of linearity which is consistent with the plot of Stokes' shift vs. the ET30. When Stokes's shift in wavenumber scale was replaced by synchronous fluorescence maximum in nanometer scale, the solvent polarity dependency measured by λSFSmax vs. Lippert-Mataga plot or ET30 values offered similar trends as measured via Stokes' shift for protic and aprotic solvents for curcumin. Better linear correlation of λSFSmax vs. π* scale of solvent polarity was found compared to λabsmax or λemmax or Stokes' shift measurements. In Stokes' shift measurement both absorption/excitation as well as emission (fluorescence) spectra are required to compute the Stokes' shift in wavenumber scale, but measurement could be done in a very fast and simple way by taking a single scan of SFS avoiding calculation and obtain information about polarity of the solvent. Curcumin decay properties in all the solvents could be fitted well to a double-exponential decay function.     

Ultrafast fluorescence studies of dye sensitized solar cells

Time-resolved fluorescence spectra from the RuN719 dye exhibit very short lifetimes (<30 fs) in solutions, on non-injecting substrates and on injecting ones. This reveals <10 fs intramolecular energy redistribution competing with the injection. We conclude that injection proceeds on a sub-10 fs time scale from non-thermalized levels of the dye.     

A novel view of gel-shifts: analysis of RNA-protein complexes using a two-color fluorescence dye procedure

The electrophoretic mobility shift assay (EMSA) is a common technique to identify and analyze RNA-protein interactions, using the altered electrophoretic mobility of RNA and/or protein upon forming an RNA-protein complex. Traditional techniques of visualization of the EMSA results include either prelabeling of RNA before complex formation or specific RNA- or protein-staining after electrophoresis. Recently, two-color fluorescent staining (TCFS) methods were developed, in which the nucleic acid is stained first and scanned; subsequently, the protein is stained and scanned. In the current study, we developed a TCFS system, in which RNA and protein are stained with SYBR Green I and with SYPRO Red, respectively. The gel is subsequently scanned in two channels in a laser scanner to detect both simultaneously. Furthermore, we show that tetramethylrhodamine (TAMRA)-labeled proteins can subsequently be monitored in multicomponent RNA-protein complexes. This novel two-color fluorescence staining is simple, sensitive, and significantly faster than other comparable procedures and allows the independent quantitative determination of both free or complexed nucleic acids and proteins. The interactions between 23S rRNA and ribosomal protein L11 and the ribosomal protein complex L10/L12(4) were used to demonstrate the advantages of this method.     

The enthalpy of fusion and degree of crystallinity of polymers as measured by DSC

Crystalline polymers are not in thermal equilibrium and thermodynamic parameters such as enthalpy of fusion as determined by differential scanning calorimetry from the area under the melting endotherm over a wide temperature range have not been measured under equilibrium conditions. Accordingly measurements of the degree of crystallinity based on the enthalpy of fusion reflect experimental conditions, are incorrect in that they do not usually agree with those determined by other analytical procedures, such as density and WAX scattering, particularly when measured at ambient temperatures. While this has been repeatedly pointed out procedures used to determine the fractional crystallinity of polymers based on the enthalpy of fusion continue to be widely used.Using the First Law method, the enthalpy of fusion and fractional crystallinity have been measured as a function of temperature for metallocene polyethylene and polyethylene terephthalate during heating. The crystallinity measured on the sample prior to heating is in good agreement with that determined by density and wide angle X-ray diffraction.     

Order parameters of dye molecules in lyotropic nematic mesophases

The alignment in a magnetic field of two similar azo dyes in binary nematic lyotropic phases (C₇F₁₅CO₂NH₄ and C₈F₁₇CO₂NH₄ in D₂O) has been studied. The order 5 parameter for the dyes was determined by measuring quadrupolar splittings (deuterium N.M.R.), the anisotropy of the electric conductivity and dichroism. The order parameter of the dye fixed in the disc-like perfluoro micelle with positive diamagnetic anisotropy was determined as a function of magnetic field strength, surfactant concentration, temperature and chain length. In addition the time constants for orientation and disorientation were determined.     

The photoacoustic determination of fluorescence yields of dye solutions

A new method for the measurement of the primary fluorescence quantum yield of dye solutions is presented. The method is conceptually and experimentally simple, relying of the S_n → S₁ transition probability as an internal standard for comparison with the S₁ radiationless transition probability, both probabilities being measured by photoacoustic spectroscopy.     

The optical properties of triphenylmethane dye molecules and chromogens

Industrial dye monomers, including malachite green, crystal violet, brilliant green, and methyl violet, were isolated by extraction with the use of heptane. UV light absorption bands characteristic of pure molecules were determined. The molecules of the dyes studied, which were ion pairs (formed by dye cations and oxalate or chlorine anions), did not absorb light in the visible range; that is, they were not chromogens. The conclusion was drawn that chromogen particles responsible for chromaticity were supramolecular dimers of nonchromogenic triphenylmethane series molecules. This conclusion was substantiated by trends in spectral transformations with the participation of immonium hydroxides obtained from dyes and side products of the synthesis of industrial dyes with quinoid molecular structures.     

Extracting decay curves of the correlated fluorescence photons measured in fluorescence correlation spectroscopy

We have developed a new method to extract the decay curves of the correlated fluorescence photons from the data of fluorescence correlation spectroscopy using time-correlated single photon counting. In this method, a two-dimensional correlation map of photon pairs is generated at an absolute delay time with reference to the excitation-emission delay of each photon. Using a dye-labeled DNA as an example, we have demonstrated that the decay curve of the correlated fluorescence photons is separated from the uncorrelated background signals simply by subtracting a two-dimensional correlation map at sufficiently long delay time without additional prior information.