Synthesis, spectral behavior and biological activity of some novel 1,3,4-oxadiazine cyanine dyes

New methine cyanine dyes covering monomethine cyanine dyes and dimethine cyanine dyes derived from benzo[(2,3-b)benzoxazine; (2,3-e)1,3,4-oxadiazine]-5,12-dione were prepared. The electronic visible absorption spectra of all the synthesized cyanine dyes were investigated in 95% ethanol solution. Biological activity for a number of selected compounds was tested and evaluated against various bacterial strains (Bacillus subtilis, Escherichia coli, Pseudomona aeruginosa and Staphylococcus aureus). Structural determination was carried out via elemental analysis, visible, mass, IR and 1H NMR spectroscopic data

Structure and electronic absorption spectra of cyanine dyes – derivatives of tetrazolo- and triazoloisoindole

The electronic structure and absorption spectra of cyanine dyes – tetrazoloisoindole derivatives and triazoloisoindole were calculated. It was shown that these dyes, in terms of their electronic structure, are trimethine cyanine, although formally they are monomethine cyanine. The electron donation of the tetrazoloisoindole and triazoloisoindole residues was determined on the Ilchenko scale, which allows them to quantitatively quantify their Bruker basicity in comparison with the most known heterocyclic end groups of cyanine dyes

Novel styryl and aza-styryl cyanine dyes: Synthesis and spectral sensitization evaluation

Novel styryl cyanine dyes and aza-styryl cyanine dyes having the nucleus of furo[(3,2-d)pyrazole;(3',2'-d)oxazole] iodide salt were prepared. Spectral sensitization evaluation for all the synthesized styryl and aza-styryl cyanine dyes was carried out through investigating their electronic visible absorption spectra in 95% ethanol solution. The dyes were thought to be better spectral sensitizers when they absorb light at longer wavelength bands (bathochromic shifted and/or red shifted dyes). Consequently the spectral sensitization of the dyes decreased when they absorb light at shorter wavelength bands (hypsochromic shifted and/or blue shifted dyes). The results discussed in this study revealed that the spectral sensitization properties of the examined dyes is highly effected by the type of the X substituted in the phenyl ring system for the styryl cyanine dyes and by the type of the phenyl and/or the naphthyl ring system for the aza-styryl cyanine dyes. Structural confirmations were identified by elemental analysis, visible spectra, IR and 1H NMR spectroscopic data

Unsymmetrical Trimethine Cyanine Dyes: Synthesis, Optical Properties, and Evaluations as Inhibitors of Protein Arginine Methyl Transferases

Carbocyanine dyes are a class of organic compounds that possess two nitrogen containing heterocycles that act as electron donors and acceptors connected by a conjugated methine bridge. This thesis will present the synthetic methodology of symmetrical and unsymmetrical trimethine cyanine dyes in three chapters. The first chapter is a review on the synthesis and application of unsymmetric cyanine dyes. The second will describe the synthesis of unsymmetrical trimethine cyanine dyes and how their optical properties differ from symmetrical dyes. The third chapter will not only discuss the synthetic procedure for synthesis of symmetrical trimethine cyanine dyes, but also will show how varying the N-alkyl substituents and hydrophobicity of the heterocycles affects the dyes interaction with and ability to be used as inhibitors for protein arginine methyltransferases (PRMTs). Several synthesized compounds have displayed lower IC50 values for the inhibition of PRMT1 and PRMT5 comparable to that of current inhibitors

Synthetic Development of Cyanine Dyes and Investigation of Their Interaction with Duplex DNA

This thesis outlines two projects that examine interactions between DNA and cyanine dyes: 1) Investigation of monomethine cyanine dye through the synthesis and optical characteristics with a goal to synthetically manipulate these systems to develop a fluorescent biological probe. Several asymmetric and one symmetrical monomethine cyanine dyes were synthetically prepared and their optical properties versus structural changes were explored. Representative dyes were selected for spectroscopically investigating DNA binding to enhance existing probe designs. 2) Early stage development of a non-metalated photosensitizer for photodynamic therapy (PDT) by screening experimentally derived cleavage activities of a number of polymethine cyanine dyes with various adjoining heterocycles. Structural characteristics of these dyes which promoted cleavage in the dark were identified and eliminated to allow for more selective photo-induced cleavage to enhance the candidacy of these compounds as photosensitizing agents. All compounds were purified through recrystallization or column chromatography and were characterized via 1H and 13C nuclear magnetic resonance (NMR). Compounds from the first chapter were further characterized using mass spectrometry

The Utilization of Alternative Synthetic Methods for Further Optimization of Cyanine Dyes and their Potential Use in Imaging and Photodynamic Therapy

The work presented in this thesis aims utilizes the versatility of cyanine dyes. Although large libraries have generated for these compounds, their remains an unmet need for alternative synthetic procedures that both optimizes and allows the dyes to be tailored for the desired use. The cyanine dye scaffold contains many points of modification but the central carbon remains a point that requires further research. In addition, among the heterocyclic compound that can be used in the synthesis of cyanine dyes, the quinoline heterocycle offer interesting optical variations to the dyes and can be utilized in the applications that do not require highly fluorescent compounds. The dyes presented showcase a superior synthetic procedure, and incorporate the quinoline heterocycle in novel compounds

The Effect of Varying Short-Chain Alkyl Substitution on the Molar Absorptivity and Quantum Yield of Cyanine Dyes

The effect of varying short-chain alkyl substitution of the indole nitrogens on the spectroscopic properties of cyanine dyes was examined. Molar absorptivities and fluorescence quantum yields were determined for a set of pentamethine dyes and a set of heptamethine dyes for which the substitution of the indole nitrogen was varied. For both sets of dyes, increasing alkyl chain length resulted in no significant change in quantum yield or molar absorptivity. These results may be useful in designing new cyanine dyes for analytical applications and predicting their spectroscopic properties

Effects of chemical structure, solvent and solution pH on the visible spectra of some new methine cyanine dyes

Some new dimethine and bis-dimethine, cyanine dyes derived from benzo[2,3-b; 2`,3`-b`]bis-pyrazolo[4,5-b]-l,4-(oxa-, thia-, and pyra-)-zine-6,12-dione were synthesized. Effect of chemical structure on the electronic visible absorption spectra of all the synthesized cyanine dyes was investigated in 95% ethanol solution. Effects of solvent and/or solution pH on the electronic visible absorption spectra of some selected synthesized cyanine dyes were also examined in pure solvents having different polarities and/or in aqueous universal buffer solutions, respectively. Structural confirmations were carried out through elemental analysis, mass spectroscopy, IR and 1H NMR spectra

Investigation and Characterization of Novel Pentamethine Cyanine Dyes for Use as Photosensitizers in Photodynamic Therapy

Cyanine dyes that absorb light in the near infrared to far red region of the electromagnetic spectrum are desirable as photosensitizers for photodynamic cancer therapy. Light of wavelengths in this range is able to deeply penetrate tissue allowing for practical in vivo use of these dyes. A series of three structurally similar pentamethine cyanine dyes that absorb light ~800 nm to ~500 nm was tested to determine the effects of structural influences on the yields of supercoiled DNA photo-converted to nicked or linear forms. Possible mechanisms and optimal parameters for near- quantitative DNA photocleavage with a symmetrical quinoline pentamethine cyanine dye are discussed

A two-state model of twisted intramolecular chargetransfer in monomethine dyes

A two-state model Hamiltonian is proposed to model the coupling of twisting displacements to charge-transfer behavior in the ground and excited states of a general monomethine dye molecule. This coupling may be relevant to the molecular mechanism of environment-dependent fluorescence yield enhancement. The model is parameterized against quantum chemical calculations on different protonation states of the green fluorescent protein chromophore (GFP), which are chosen to sample different regimes of detuning from the cyanine (resonant) limit. The model provides a simple yet realistic description of the charge transfer character along two possible excited state twisting channels associated with the methine bridge. It describes qualitatively different behavior in three regions that can be classified by their relationship to the resonant (cyanine) limit. The regimes differ by the presence or absence of twist-dependent polarization reversal and the occurrence of conical intersections. We find that selective biasing of one twisting channel over another by an applied diabatic biasing potential can only be achieved in a finite range of parameters near the cyanine limit.Comment: 45 pages, 9 Figures (incl. 2 chemical schemes). Accepted for publication by the Journal of Chemical Physics. Changes include 2 additional figures to and expanded discussion of key points felt to be important, and condensed discussion of some points felt to be less importan